This is just silly. Knowingly planning to and actively harming someone is malicious. AKA, planning to ghost someone while clearly being shown to realize how that will affect said person.
Yes, that's the joke. GennArc and I think Yami was being honest at this point. Or at least he expressed that opinion in the past; I don't know if he changed his mind. That Yami wasn't planning to ghost Yuu at this point, even if she felt disappointed and hurt by his —apparent— lack of reaction.
What happened to cause such a radical change in the mini time-skip between chapters 28 and 29 was that Yami received a phone call, probably at the beginning of the second day, notifying her from the hospital about her mother's suicide attempt. This is what changed everything. This is important because Yami is never fully capable of lying to herself or to Yuu at the same time (for example, in chapter 23 she can lie to herself, but her words to Yuu leave clear she was really interested emotionally in him and as a good tsundere she didn´t want to recognize it).
His pressure to demand honesty about her family affects her deeply emotionally, this is symbolized by his gesture to squeeze her fingers after she holds his hand -as a symbol of their femdom relationship-. Therefore, when her thoughts and words are aligned with her genuinely believing that everything in her family is resolved and that she can stay by Yuu's side, she's being honest.
The scene where she acknowledges to herself that she is lying when she calls Yuu "I will make you my boy toy" - and yes, she uses that derogatory term so that Yuu realizes that she is lying, and he does - is an example of how in the previous scenes she was honest and sincere with him.
Both done by the same person you've tried to claim was "harmed" by Yuu by incorrectly claiming that he "rejected her" and wasnt taking the relationship seriously lol. These are active actions, implying that that he was knowingly hurting her (of course he never hurt her at all).
Ayami is, in theory, even worse than an openly malicious person (except for chapter 33 and her final action in chapter 40, when she decided to kiss Yuu after seeing the cowardly Hikari spying on them at the door). Ayami is a mentally very unstable girl after all the trauma she suffered,
and it's clear she doesn't know what she really wants or desires. Worse still, she doesn't know how to directly express her feelings to Yuu, which is why she resorts to sex to show with actions what she can't say to him with words —and he correctly detects this and attempts to see through her mask and fix her.
That's why she not only wants to hurt others, she wants to hurt herself as well. That energy of "we will inflict deep wounds on our hearts, Yuu". And precisely because she is being sincere in several points and she really loves him, she ends being more toxic and abusive with Yuu than she would have been if she always would have planned manipulate him and later throw him. So, she cannot love Yuu if she cannot love herself.
Hence, she's serious about Yuu, but she can't fully open up to him emotionally, she can't fully express her true feelings to him neither trust fully on him. That's why Yuu constantly pressures her to have a formal relationship, and most importantly, he succeeds, which is why Yami calls Yuu "my boyfriend" in chapter 28.
And the funny thing is, this also happens in reverse; I think that's what GennArc is saying.
I'd like to see the mental gymnastics you'll pull to make it seem like Yuu is in any way at fault with that while downplaying what she did.
Objectively, IMO, Yuu didn't hurt Yami, but he also failed to fully convey to Yami how seriously he was involved in the relationship (and again, it didn't help that Yami is, ahem, crazy). That's why we see in chapter 26 the fears of Yami that Yuu is only with her because Hikari sent him to the friend-zone.
That's why Yami gets upset by Yuu's apparent lack of reaction in chapter 28. In that scene, whatever he was thinking, it was undoubtedly that obvious lack of visible reaction that made Yami think he wasn't taking her offer seriously. If Yuu wanted to hide his thoughts behind that poker face Yami taught him to use, he completely messed up here. Which, of course, still doesn't justify Yami's subsequent actions at all. But let's accept that Yuu did make a mistake here, and that's perfectly understandable, and that it was Yami's responsibility to clarify that she was serious. Out of her own tsundere pride, she refused to do so and instead turned it into a "joke."
Yami's actions in chapter 40 are also more of a mental breakdown than a deliberately malicious intention to hurt someone. She makes it quite clear in her internal monologue, both in the novel and the manga, that she knows she's being incredibly unfair to Yuu and accusing him of things he's not actually responsible for, expecting him to be some kind of fairytale prince who would magically find her during her ghosting, with her actively avoiding him. It's hypocritical and immature of her, and as already mentioned, other proof that she should be in a psychiatric hospital right now.
There is a clear distinction between someone acting with the intent to harm someone else and someone getting upset at circumstances. This is an objective distinction, btw. Any rational person can see that.
Yes, that's the joke; Yami is anything but a rational person right now. The girl believes Yuu hurt her when in reality he didn't, and she knows perfectly well that he's actually innocent of her incoherent accusations of "not fighting hard enough for me." It doesn't help that Hikari, the masochistic pimp, did show more of that "resilience"—and yes, this would be the upside of Hikari's emotional insensitivity; it made her more capable of dealing emotionally with "Aya-chan."
And yes, just because you will have people arguing that gravity doesnt exist doesnt make it any less an objective truth. These two things are different. You may be a weirdo who treats someone being harmed by circumstances (indeed circumstances she created) as being worse than someone actively harming another when ascribing blame, that may be your subjective rating, but they are nonetheless objectively different.
Genn never said Yuu is worse than Yami in any sense, and I dare you to show a quote when he really says in the page Yuu is worse than Ayami. He only said maybe Yuu is not 100% innocent and non-guilty by the collapse of his relationship with Yami, even if the main fault is still from her. However, it's silly to blame him for being a 15-year-old boy who doesn't quite grasp a hint, which is a fairly human and understandable mistake on his part, and it was Yami's responsibility to clarify that she was serious.