You have a campaign that provides, by design, a high level of freedom for the players to pick the story threads, sides and whatnot for themselves.
In the long run, a conflict arises: some player characters wish to side with / follow X while the others want to side with / follow Y, which is the opposite of X. (An example: you're playing Star Wars with freelancers who after a year or two decide to join A) the Rebellion, B) the Empire. Please keep in mind that this is just an example, the question is not SW-specific. It could be Lannisters vs Starks, cultists of Cthulhu vs the good guys, whatever. Also, there's no definite moral supremacy on either side, despite what these examples suggest.)
How do you handle such a PC conflict without being too intrusive on the choices of some?
How do you keep the group together (if you keep it together after all)?