A little update, I'll probably update the main post soon-ish. First, someone on Reddit found out and told me about a way to complete Space-Crime Continuum without killing any of the bugs, among some other things:
This is nice! With that done, the rest of the quest is beatable, as are The Ice Palace and The Chimerist's Last Experiment -- allowing you to bring this questline to its conclusion. I haven't replicated it in-game for myself, though.
On the more, uh, technical side of pacifism, ymfah did a no-kill run of the game and wiped out Edgewater without shooting either the people