Ever heard of victim blaming? This really isn't any different from seeing a woman who'd suffered from psychological abuse, who spent years convinced that her boyfriend/husband was completely right and she deserves the treatment she's getting, and saying "she could have said something or stood up for herself, she's just as much to blame for this as her husband is!" And no, he did clearly believe what she said up until he finally left her. He followed her orders and believed what she said, believed that no one would side with him, believed that people would react the way you did or even just dismiss him outright. The problem was that Hanabi pushed him past the threshold. She'd managed to keep him for years in this state where no matter how badly she treated him he was sure others would treat him worse and losing her as his "support" would just lead to an even more hellish existence. But being forced to push himself to the point that his life was in danger for a laugh finally convinced him that the future she insisted he'd have without her, alone and outcast and hated by all, would still be safer and less painful than staying with her.
The recent plot was definitely over the top. I can see the idea behind it, as I said of her being convinced that her actions carry huge weight, that the ways she'd put him down were so extreme they'd ruin his life, despite the fact that someone who'd really stayed on Souma's side and watched his friends with something other than self-centered jealousy would easily realize that the guy's life is now built around individuals who would see those clips and not feel any contempt, pity or other unwanted feelings toward him. Good lesson for her, but badly executed and really didn't need to go so far as rape and prostitution.
And that's not to say I think Souma is entirely correct. I think he's in the right, but he's not judging clearly or correctly as he has an understandable bias against her. After more than a decade of abuse, he doesn't believe she can care about others or that she can be sincere about her regrets, and so when she apologizes or even grovels all he can see is a big public act designed to make everyone look at her and pity the tragic heroine. This is clearly not the case, and it seems like Yukishiro realizes this just like she realized there was a form of love in Hanabi's actions back in 30. Like I said before, she's not like he believes, a drama queen who's desperately trying to make herself the main character regardless whether it's a love story or a tragedy. She may have been a bit like that in the past, but she's made it past that and seems to hate that past behavior. She just needs to grow a bit further and realize that she indeed CAN live her own life without worrying. She's basically treating her past abuses as an unforgivable sin that ruined Souma's life rather than a cruel experience that ruined their potential relationship with one another. If she can get that through her head, she will indeed be able to move on, find her own path, make friends who exist for reasons unrelated to her relationship with Souma, get a boyfriend who's not just there to make him jealous, achieve a future career and lifestyle that is completely separate from him and not at all unfulfilling for that.