Something that should perhaps be explicitly mentioned considering it runs counter to how a lot of other games customarily run: There's no reason why a PC can't be a dark sider and continue to work with the party if they're willing to put up with their behavior. This isn't a system where it is expected that a character that goes "Evil" will turn into an NPC, provided your group hasn't set expectations about tone and story that make dark side behavior disruptive. You should still, of course, have there be in-world consequences (good and bad) for behavior, but those don't need to be punitive. After all, there are plenty of bounty hunters, crime lords, dark jedi, and politicians who enjoy long, successful careers before somebody sends them tumbling to their demise.
(I realize this is a bit redundant with what people are saying re: Conflict not being a punishment, but I still think it's worth stating directly.)