I would help the rebels, it's always cool to fight against the law. That would be on my first character, of course if the story is branched and I can get different events for each choice, I'd support the other side too with the other characters.
Pardon my ignorance, but where has it even been confirmed that the Nord's civil war is because one faction wants to leave the Empire, and one faction doesn't?
Confound it all. This is what I get for ignoring most info about Skyrim and then opening my mouth.