On the replacements, I do think Trigger should have been either replaced earlier or (if no replacements were available) modkilled. Include would also have to be modkilled, can't treat scum differently to town.
Natiko you mentioned something about Include being replaced because it wasn't her fault she had to leave, or something along those lines. It sounds like you would view a modkill as a punishment in that situation, which is wrong. Modkills are just a tool, unfortunate when they have to be used but necessary for the health of the game. For all we know Trigger's absence could have been just as unavoidable.
I don't know what the "rule" should be and I don't even know if it's something you can set hard in advance, but something about being that close to lylo should discourage replacements from happening.
I also disagree that replacements should be held to a higher standard than anyone else. Replacing is hard work, I don't think we gain much by making it harder.
As for the hostilities... I don't know if anyone should have been modkilled or subbed out, that's always gonna be the hardest decision to make. I have to agree with KetKat that the number of people subbing out (or considering it) due to the extended hostility is kind of self evident. Perhaps a firmer hand would have improved things, perhaps not. I agree with you when you say there's no solution that everyone would be happy with.