The irony is that was a last-minute line I added that really was never part of my original plans which is why the reaction reads so wrong. I could go remove it because it doesn't have any impact on the story going forward but everyone already past that part will never see it. So I still have to try to dig out of that hole.
I wouldn't see it as a 'hole', its just part of the writing process. Its iterative, not everything comes out perfect on the first draft.
Sometimes things that sound right initially you later realize read differently to other people.
So with that in mind I also don't see making changes as caving in to other people's desires but rather making sure the story you tell comes across in the way you intend it to.
Obviously you know how the story goes but the readers don't, yet, so its potentially easier for you to rationalize dialogues or inner monologues with how things eventually turn out while the read is just taking it on face value.
Another thing to consider is people rarely take the time to give detailed feed-back or criticism on a story that they otherwise don't see any potential to, so the fact that people are commenting on specific aspects but still generally wanting more I think should be seen as a positive.
If you consider that most of the feed-back, from what I can see, seems to be how the MC reacts to situations with or the revelations from those around him, particularly from people he should have been able to trust implicitly, then I think you're generally on the right track and readers don't seem to want to actually change the story, rather they just want more authentic or believable MC responses/choices, since so far the MC just seems to go along with most everything without being too bothered.
For example it was good to see the MC finally get in contact with Anna, because after learning about both her and the MC being memory-altered I would have though the MC would have attempted to contact her immediately.
So again i think you're on the right track, the story is decent and has a lot of potential and I think with some iteration on the MC's reactions to what should otherwise be disturbing situations or revelations you'll be doing just fine.
Oh also if you do make changes to previous content, just let us know in the change-log and I think anyone who is interested will replay that content to get the new dialogue or whatever it happens to be.
I mean I already replayed this update from the start anyway since it'd been a while since the last update and I wasn't sure if I'd remember all the previous events anyway.