I'd suggest you to read infocards and whatnot. The Royals use the Corse as Bounty Hunters of sorts, and they also have close ties to the Police, through bribes and whatnot. Not all is white and black, the Corse are a grey area. We may be criminals, but we have our place in the Gallic society. The same goes for the Hogosha in Kusari: they're often considered to be criminals, but they are not enemies of the state. They have their uses, so the state closes their eyes on -some- of their acts. If they,re caught doing a crime though, you can gladly kill them.
Also, while we're listed as allies of the Brigands and the Maquis, we also have to shoot them once in a while as we're requested to do such by the Royal navy or another such entity. To correct your statement as well, the Corse has little relationships with the Council and prefers to stay neutral in the revolutionary conflict, instead playing both sides to make profits.
If you'd bother reading around instead of shooting all "Red is dead"-like, you'd know this kind of stuff.
