Civilians tend to out themselves by vouching for one another. That's just something you're going to want to limit is all. No major reason you couldn't include two.
I have plans for a Mega Man Mafia, by the way. My favorite series growing up.
Too many civilian kills. There probably shouldn't be two groups of civilian BTSC. Hal can kill but knows who everyone is, which means he can take out the killers and BTSC guys first (that's what I would do). Balance is indeed hard to assess because you have a clusterfuck of a game here. Not bad if that's what you're going for, I guess.