In this style of game, with continuing storylines pertaining to the global history, i don't like alternate endings. But then again, i never liked Choose Your Own Adventure books either... I don't think they should be done, as they diminish the joint experience in the continuing world.
As far as the Civil War goes... it's actually easy. No one wins. It's already set up in the questline in-game, where regardless of your side, you are told that the opposing party remains, and the conflict will continue. Either way, you just take out one leader, but their are others.
IF they pick a side, i won't be overly upset about it. I mean, i played Humans in Warcraft 1, and the story for 2 continues from an Orcish victory. It's one of the consequences of having a flawed A or B situation.
The games tend to be open enough that both endings are plausible...in Skyrim. The Imperials could win, sure, but they could just as easily make it so that the Emperors death causes Cyrodiil to spiral out of control, recalling the Legion stationed there, allowing the opposing faction to oust what little support they would have had after being abandoned. The same goes true for a Stormcloak victory.
I expect things to get worse for the Empire rather then better, but we'll see.