I think the purpose of Io's scene (at which it was quite successful) was to cause a reaction of visceral disgust in the player (and hopefully Akira) in regards to the way Akira uses sex. Akira resorts to sexual contact both as a defense mechanism and as a crutch to avoid connecting on a more emotional level. On some intellectual level he knows this is a morally wrong, but up until now he's never had a reason to actually believe that it's wrong. Every time he starts a sexual relationship with a girl, it does successfully lead to them growing closer and even to an emotional connection that he doesn't have to work for. Even his most heinous actions (with Ayane/Kirin, Nodoka/Yumi, Molly, Ami/Noriko) involve him being a more passive participant, and have generally just led to him growing even closer to his victims in the long term.
I think Selebus is trying to beat us over the head with just how destructive Akira's mindset is. As such, I will be absolutely shocked if this leads to things improving for Io, even in the long run, since that would undermine the scene's narrative purpose. I expect this is the first step on Io's path to becoming absolutely broken, if she isn't there already. I'm expecting to see an Io with "wishing well eyes" sometime soon.
I do have concerns as well for what Sel's aversion to branching narrative means for the future, but not as much for Io's story. I think he can handle that with a bunch of missed events until the point where the branches are brought together again when she is inevitably reset. I'm sure it will lead to a less cohesive narrative if you decided to leave, but for me that's fine. Sel is telling a linear story, but the fact that choices exist in the first place is integral to his narrative method.
What does concern me is how Sensei's character development and the overall plot can progress if he decides to leave. I think he needs to break someone with "consensual" sex in order to move forward. And with all of SekaiDolia's talk of breaking people in order to fix them, it seems like Sensei needs to observe someone being broken and reset as the first step towards what I'm assuming the dark path is going to be. So I just don't see how the plot can move forward after leaving, even with missed events and a lack of narrative cohesion.
How are people interpreting Ami's scene with Uta? At first I thought that Ami was probably acting in order to deflect having to talk about Sensei and Uta's picture, but then Uta leaves the room and it seems like Ami did actually want something to happen. I guess it makes character sense for her to be secretly bi, she wouldn't have wanted to admit the possibility that she could ever be sexually interested in anyone other than Sensei.
I need to mull over the supernatural stuff in the update more before I post about it, but I want to say one thing for now: I've seen some people commenting on Yasu telling Sensei that he needs to swim, but I'm like 99% sure that's actually SekaiDolia speaking. I'm not sure if Yasu and Touka are even physically present in "The Art of Drowning" with the way that they dissappear, it might all be in Sensei's head. If they are there, Sekai is talking directly through Yasu the same way she does through Kaori (which was probably enabled by Yasu touching Kaori at the end of the previous event).
