Yeah, considering how many life and death situations he's been through by now, I feel like reflex would have made him drive the blade home. Feel bad about it afterwards, but when the adrenaline is flowing, you don't have time to think.
That's actually the whole point of this situation: He wasn't high on adrenaline, but able to remain calm and focused and exploit his much stronger foundation to the point he could afford to take them non-lethally, rather than having to kill them all.
This is not a status screen world, the murderous bandits charging you do not have convinient "level display" floating above their heads. Why do you think he can judge the danger level of humans, that you said yourself he has no experiance fighting against, in order to feel he has room for mercy.
Even if he could judge the danger level, a lucky throw of a small axe could easily inflict a letal wound even on MCs OP self if he didn't have plot armor. Even with bullshit healing fungus, dead is dead prb?
Yeah the first kill might be traumatic, but difficult? No, not at all, when someone is trying to kill you there will be ZERO toughts in your mind that say "I better not kill this person" unless you're an evolutionary anomoly. Your brain will be fully occupied by protecting your own "life", an instinctual action that not only is hard to resist but also nobody would try to resist.
Peace era orgins btw, that's manga talk, even in the modern world you would defend yourself way before worrying about excessive force, exception possibly being people doing judo and the like against specifically unarmed opponents. As soon as someone pulls a weapon that consideration is out the window, both on a personal level and mostly in the eyes of the law too I'd wager.
Though many "modern world people" would understandibly consider their best defense to be NOT fighting, an act that would be suicide in a society without sufficiently dense population and oversight like the one MC is in.
The same way he has been judging the strength of every other enemy he's encountered so far, with the danger sense born of the spores in his body towards things that are stronger than he is. He's also taken much worse blows than those able to be inflicted by a throwing axe, even putting aside his insanely good self-regeneration; they aren't a threat to
him, but a threat to the driver and the other hunter.
The first kill is way harder than you are making it out to be; no idea where you're getting this, "It's easy to kill other humans" BS from, but it was something that came about as part of seeing only the people of one's tribe as people, and others as less than, which as a modern-era human he doesn't have that mentality
at all. Especially given his exceptional strength and skills that allow him to suppress the enemy nearly single-handedly, non-lethally. It's also not "manga talk", it's real-world talk. Most people DON'T defend themselves before worrying about excessive force, unless they're panicking (like he did at the start of the manga), which he is not doing here. He is going into this situation entirely pre-meditated and more than able to kill, but with more than enough power to not have to, as well, thus the hesitation, and the non-lethal (or I guess we should be using "less-than-lethal", but everyone understands that the former means the latter anyways) means used to incapacitate.