@Ceildric I don't think it is pathetic at all. It is the only possible answer for Tanikaze. I have the impression that many of the points in KoS flew over your head from your comments. I'm not that big of a fan of this series, but I like how Sidonia is a criticism of militarism through the military point of view. It is a study of the impossibility of communication between humans and aliens without giving clear answers, only implications that allow us to draw countless conclusions and interpretations (clearly inspired by Stanislaw Lem's Solaris). It is also about the next step of human evolution: the symbiosis of two races in a millennia war. If you look deeply into it through the mainstream appeal filter, there is a lot to reflect on. That's one of the reasons that make this author's manga fascinating. He wants the reader to think for himself. KoS benefits significantly from a reread.
Talking about the mentioned scene: Tanikaze cannot admit that Ochiai has a good point and try to counter it because he is not a scholar or scientist, just a soldier. Ochiai's speech makes him hesitate (to the point of listening to him!), thinking about what Kunato had revealed earlier. Still, in the end, he accepts what he is: a soldier, a weapon for Sidonia (a Knight), and nothing more. It doesn't matter if Ochiai is right or not; there is nothing he can do. His mission, the reason for his existence, is to carry out his superiors' orders to ensure Sidonia's survival. It's all about killing to secure self-preservation.
Ochiai's and Kobayashi's philosophical conflict started hundreds of years ago, and since then, it has become impossible for these opposing ideas to coexist. The only possible resolution is that one side would have to swallow the other to survive. Ochiai failed to do so. History repeats itself, and Tanikaze put an end to his existence, once and for all this time. It is somewhat tragic, but Ochiai himself also has his share of guilt for his uncontrolled ambition and eventual self-indulgence (even if it is for the greater good, in his POV). Kobayashi is not so different, just another side of the coin, since she monopolized Sidonia's government and even put an end to the Immortal Council. However, she has softened throughout the narrative (partly thanks to Tanikaze, which made Kobayashi remember her pre-immortal, youthful times) and has become (ironically) more human and less self-centered.
@Highlander1 Thank you for responding at length, and raising at least one interesting point which I will admit I may not adequately factor in. You may get the impression that the series "went over my head" or that I did not try to take it seriously from some of my meme-ish, half-serious remarks throughout the series. Those are reflective of the mood I was in while reading, and also the disappointment I had in the series. If you would like to read my more extensive and more serious thoughts on the series, I posted in https://mangadex.org/title/1337/knights-of-sidonia/comments/ after I was all done.
That said, I am not denying I could have missed something. In fact, that is the point I liked most about what you wrote. Essentially, I think it may be possible that, as you seem to imply, Knights of Sidonia may be more of an experiential piece, so to speak. Perhaps as you seem to be saying the author was trying to say something about militarism and/or communication with alien species and decided to do it by way of what I would call caricature. Maybe we could generously call this impressionistic? I don't know, I am not an art critic.
I am very much a fan of manga (and movies, books, comics, games, etc) that invite readers to think for themselves. I much prefer an author lay out situations with complex view-points, lots of grey, and little preaching on the author's part (unless he can do so while intelligently addressing possible counter-points). I am considering that it is possible I have a preference in what style that takes, how it is presented, and may not fully be appreciating Knights of Sidonia for that reason.
However, let us look at the specific moment I called out, Tanikaze's response to Ochiai.
I called it pathetic because I believe his response is that of a slave or an automaton, not of a soldier.
Even if we were to go with the common soldier stereotype / trope to lampoon militarism, I would expect a soldier to be able to muster some justification that goes beyond, "I have no choice." Perhaps he could have said, "I am a weapon, and it is a weapon's function to serve it's master." You might say that sounds like slave thinking too. In a sense it is, but it shows that the speaker at least has reflected on the situation, has adopted some kind of philosophy or justification. One may argue whether it is their own or the product of propaganda or the like, but that is another question entirely.
There are other possible response too like, "I don't care about the evolution of the species if it comes at the cost of my friends." Or "I won't betray my oaths / honor" (kind of similar to the above about being a weapon). Or even something like, "They attacked us first."
The bottom line is that I think that if it's meant to be part of the supposed critique of militarism, it shows an extreme naivety whereby the author apparently thinks that soldiers are so mindless that they do not even reflect on their actions or the wars they're in, and cannot even parrot the position they have been no doubt taught by their military or political leaders, let alone offer some rationale themselves. One can absolutely doubt, question, pick apart the rationalizations for war (in general or specific) and plenty of great works have done so, but it shows a naivety and disdain which (in my opinion) undermines one's argument, to reduce it to nothing as here. Of course, that's assuming that this was meant as a critique to begin with.
The other problem I see is that Tanikaze is not generally set up as some militaristic moron or deconstructed hero. He received training from his "grandfather" since a young age, but his "grandfather" also clearly was not one with the overly militaristic ideals of Kobayashi. It's not clearly exactly what grandpa's positions were, however, since that is one of many details the author annoyingly fails to reveal. That would certainly have shed more light on the dynamics of things. Regardless, I think it is safe to say that Tanikaze was not raised to be a slave to Sidonia so to speak, as his "grandfather" clearly rejected being one.
Likewise, again and again we see Tanikaze push back on orders, occasionally disobey them, wrestle (albeit in the vaguest, half-assed sort of ways) with questions about the place gauna, clones, ai etc have with humans. And after this final battle
we do not see a Tanikaze bearing regrets for killing Ochiai or the gauna. Nor do we see signs of him becoming a hardened career soldier. He seems to get a very happy ending that the audience is meant to feel quite comfortable cheering over. That's not in-line with a hero we are meant to pick apart.
Thus, I feel in this moment (and perhaps in general), Tanikaze was a pretty pathetic individual. The critique of militarism is childish, inconsistent, and/or not present.
P.S. One final thought that I just had and am not going to try to go back and work in but... Kobayashi killed the immortal council. That's certainly an example of her extreme militarism (and indeed she did it to facilitate her genocide on the guana). And yet, it's never brought up again by any of the characters in any context. It was a plot point I found really interesting and full of potential (indeed I wanted the whole dynamic with the council to be explored a lot more) but nothing. I would expect if the author was aiming this as critique of militarism that her killing the council would come up again, and that other characters would not just let her become their buddy with nothing said (let alone political tensions, unrest, a trial, something). In the end she ends up just one of the gang relaxing in a hot tub.
@Ceildric Something that perhaps contributed significantly to your disappointment with the series was wrong expectations. Knights of Sidonia is a complete space opera, mixing sci-fi mecha action and cosmic horror with slice-of-life romantic comedy. Even though the series is raising intriguing questions half of the time, speculating about humanity's future, and throwing incredible sci-fi concepts in the reader's face, this is only part of its essence. The other half is a romantic comedy (with drama) focused on slice-of-life because it is self-conscious in juxtaposing its darkest and most profound moments with young teenagers' daily lives (and other members of the spaceship) in this grim future. After all, despite the war against an almost unstoppable alien force, humanity is still functional. People still live in a semi-utopian society inside this massive cocoon that simultaneously brings life and works as a superweapon to guarantee an entire species' survival. I would say it is an intriguing take on neo-seikakei. I mean, Tsumugi has an essentially phallic form, and the author knows it, and he knows that the audience knows it. Even the characters make fun of it at one point. I'm not saying that this series is genius, just that an obscure author playing with standard tropes in the medium created a peculiar manga that works, in a way? I mean, it's not a harem series. Still, it has elements of the genre in the most exotic way possible. The protagonist engages with a non-binary person (who eventually turns into a woman), androids, an alien placenta, and even a chimera, resulting in intriguingly weird moments. Tsumugi is the heart of this series. About your criticism surrounding "things happen because the plot says so" or that Sidonia explores few things appropriately, disagreed. I do agree some stuff was left vague. Overall, the series did a satisfactory job with world-building and developing several of its ideas for the audience.
Regarding the Tanikaze phrase, I think it all boils down to the this: he is not a slave, so to speak, he did question orders and did stupid things in the past, but our hero remains a soldier, not because of a chauvinistic nature, or brainless existence, but because he de facto has no choice. What could he do? Let Ochiai go and maybe one day return and threaten Sidonia? And what would become of him after all this? Nevertheless, many hypotheses give me the same path: he had no choice because, for the survival of Sidonia and his friends, of all those people he swore to protect, he needed to kill him. It is not as if he did not reflect: he stopped to listen and remembered Kunato's words. But as I mentioned, swallow or be swallowed. His "grandfather" didn't want to be a soldier forever, and one day he finally got tired of war and sought eternal rest. Still, since they created a clone of him for the sole purpose of being a weapon, he decided to educate him to protect the people of Sidonia in an honorable way (as he says to Kobayashi).
In the end, the point is that Tanikaze is simply a young man who, until recently, had no social contact and is very naive. He is no godly-written character, but I think the author did well to show that "Look, Sidonia's government created Tanikaze with the sole intention of waging war and serving the extremist human leaders. Nonetheless, he is a teenager, raised far from society, knows little about the world, and eventually has numerous social experiences, learning to interact with people very quickly while taking unexpected and often stupid actions. Simultaneously, Tanikaze received training all his life to be the most reliable soldier possible, not for glory, but to save people, to do the best for others."
In the end, killing Ochiai was the best for everyone. At least, everyone on Tanikaze's side. He has no choice but to kill Ochiai for Sidonia. He is a soldier, and that is his mission. He doesn't regret it or become a warmonger later. Tanikaze did what was needed. He was a soldier because they needed him to be, and he knows it, that's why he does it. But thankfully, he broke out of the shell after putting an end (for now) to the war. In a way, he followed his grandfather's footsteps. So I see no problem with his phrase. He's not pathetic. He's just a young man trying to do what he thinks is best for everyone he loves.
Regarding the Immortal Council, it served two purposes in the grand narrative, the first being that it helped to characterize the morality of Kobayashi very well until that point (which contrasts with the less selfish person she would become later). And secondly, it gave the necessary autonomy to do whatever the hell she wanted inside the ship, which, as you know, led to countless disasters, including the creation of the chimeras (repeating something that she KNEW had not worked out very well before). It was an event that had real consequences within the plot, even if not directly because all that happens inside was a secret, and indeed, no one out there would end up knowing, since she took care that it did not leak. I see no problem with how the author handled the situation.
Also, check this out; it might give you an interesting perspective about what I'm saying about war critique.