my name is catte: I don't think so... assuming that both of those mafia factions know each other exist (because it's part of their win condition), if they all survived up to a point in the game then they could just claim in order to win.
GameRacer: Maybe make a no faction claiming rule in such case to prevent this?
This will be practically impossible to implement. And won't solve the issue: when do you want Mafia to win?
People with same condition are essentially on same team, no matter how you call it. I mean we can have 2 Town factions of 4 players, or put each Town player in a a separate Town "faction" and it won't be any different from having a normal game. The setup SPF described is the same as having a single Mafia faction whose members don't know each other.
Roleplay aside, same win condition = same team. By definition.
EDIT: Not saying that it's a bad idea for a sestup. Could be quite interesting.