Speaking personally, I respect thematically dark material considerably more than I actually enjoy it, so take what I'm going to say with a grain of salt. But to me, it seems like your reasoning is flawed.
If death or rape is meant to explain why the MC is in such a bad state at the start of the game, then it allowing our choices to avoid the death/rape is effectively breaking the game. As much as I prefer to keep everyone alive, I don't see how that can be a good option if the price is narrative cohesion.
And I do feel like the story lost a lot of cohesion in this update. The MC quips from his hospital bed that things couldn't have gone much worse while I'm sitting here behind the keyboard amazed everyone got off so lightly. Susan genuinely seems to believe it's her fault when a guest at her hotel is kidnapped far from said hotel. Even the disappearance of Anna feels like it should provoke curiosity more than it would anger or dread - all the more so since we in the audience already know she survived.
Would I prefer it if the situation had been much bleaker and the MC's discombobulation made more sense? Well, I'm not exactly rushing to replay the game to find out, so presumably not. But I'm still significantly less invested in this game than I was a chapter ago even though things ended relatively well, so I do think something has gone wrong here.
IMHO, you need to refine your vision for the game a little. If you really feel that serious psychological trauma for the MC is important to the story you are telling, then you need to commit to the bit. Crank up the trauma even when we make the 'best' choices and accept that some of the audience might not be able to stomach it. You don't need to go overboard; there should still be some happy moments amidst even the worst tears. But you do need to ensure the MC is well and truly raked over the coals in every scenario.
Alternatively, if you want to preserve player choices that can save characters from their fates - and this is certainly the approach I would prefer you to take! - then I think you need to relax on the bleak tone in the aftermath when we do manage to avert the worst. Yeah, everyone is going to be on edge, but they there needs to be a strong undercurrent of relief mixed in with the fear and confusion. IMHO that just did not come across in the game as it currently stands, which makes the accomplishment feel invalid.
On a tangentially related note, I also really hated the MC's interaction with Joseph. I have no idea why the MC is so obsessed with him. Like, I get that Joseph is supposed to be bad news, but the MC still acts like he's the devil incarnate even though we haven't actually seen him do much of anything yet. This is made worse by the utterly braindead way in which the MC insists on "confronting" him over and over again, only to throw a temper tantrum when Joseph fails to cower before our righteous accusations. Like, what exactly is the MC thinking here? If Joseph really is some criminal mastermind then running off half cocked is obviously going to play into his hands, and if he isn't a modern Moriarty there's no reason to keep going after him.
Maybe this would make more sense on other paths, but in my game it got to the point I found Joseph marginally more sympathetic than my own avatar. I doubt that was the intent. I'm sure Joseph still has a role to play in the story so I get why we need to establish the antagonism, but could we at least get a choice to skip the final meeting with him in this chapter?
Anyway, those are my immediate thoughts after playing the update. Take them for what they're worth.