Actions should have consequences, yes, but there should always be a way out for those with wit.
Just like how America sells arms to the Middle-East, i hope if Bethesda does implement this kind of faction mix-matching, the game is at least aware of this and has dialogue and options that are available to the character. Recall threedog's response in FO3 when you already had found the location of your dad before doing his quest.
While I'd prefer to create one character and simply do everything with him, I'd be all right with Morrowind or New Vegas-esque divergence if it was implemented better. The irritating thing about New Vegas was while the main quest breaks off into four directions, each direction is composed largely of the same quests, albeit completed for different people.