I had a very similar thing happen, where the entire Sanitorium turned hostile and the Soul in the Stone did not want to speak to me any longer, although I believe the quest NPCs did not turn hostile. I happened to threaten to break the legs of our friendly soul thief and Azo the animancer asked me What had I done, and I proceeded to dispense justice upon him as well. I had just assumed it was because of my violent choices that the entire place decided I was a threat. If it was a bug that would be disappointing as a narrative matter! Could we have a dev say whether this is a bug/not bug at the very least?