Roughly 50 hours of play earlier I decided to clean up the Tchortists I mentioned, nobody cared much, there weren't any messages telling me that was a bad thing, and their loot was great. Well, now I've discovered the sequence to get into the Institute and Deep Caverns is broken as Efreitor Denzil will emerge after the cutscene and everyone in the hall is hostile to him and shooting him to death before I can give him the Reaching Man. Riveting stuff.
Now I like this game a lot, it's my favorite release in many years, but this is pretty bad. The game so far lets you clean up entire cities if you want and suggests freedom and so on, but for some reason killing 3 nondescript masked guys can break the main quest without a word of warning, up to 50 hours of gameplay later. Please tell me there's a way around with at least a hack or something to reach Deep Caverns and complete the main quest on a character that already has 115 hours racked up going from what Steam says.