This never even occurred to me before. I started up the defending Whiterun quest, and as the battle started I just left. ran past the stormcloaks, did other stuff instead. I wanted to see if they would win without me. of course, they did.
What I didn't expect was Tullius' reaction. He said they didnt reward cowardice. He didn't give me the normal reward item for the quest, and didn't raise my rank in the legion. But I still can keep doing the quests.
I was not expecting any of that. Im sure i can keep doing the civil war quests to completion, but im curious to see what happens as far as my rank and such is concerned.