I've actually been thinking about this a lot- choosing a side in the civil war can easily be solved when the war ends without result to combat the rising influence of the dragons. This is more likely than actually ending the story in different ways (two or more) and having another Warp of the West incident- which I think you can get away with only using once in your lore anyways...
Back in 1940's China, the nation was engaged in a civil war. On one side you have the nationalists, who believed in democracy. On the other you have the communists. Both sides were adamantly opposed to each other on basic ideologies alone. Yet when the Japanese invaded during World War II, both sides set apart their very conflicted differences in order to fight their mutual enemy side by side. Unfortunately, the civil war resumed immediately after the defeat of Japan.
That is the same situation I forsee happening in Skyrim. What we know is that the civil war will play a part in the story, but the most important piece, the dragons, cannot be ignored. Inevitably, the player must defeat Alduin and save the world. During this segment of climactic world-saving, I doubt the opposing resistance and imperial forces would continue their conflict. There is no point in fighting over Skyrim if there will soon be no Skyrim left to fight over.
When it comes to ending the story, it would have to climix with the defeat of Alduin. They would not allow the most exciting part of the story become swept underneath a postponed civil war. So I believe we can put aside any notion that this civil war will have a clear outcome. So, how will it end? Will it be based on player support throughout the story? Will the two sides compromise and end their conflict on middle ground? Will the actions of Alduin and the near-annihalation of the world make the problem just go away? Or will we never find out, and simply be left wandering a region with an uncertain future like Oblivion?
Who knows.