I think it would be a pretty crappy concept of a Civil War if there if the Rebels are portrayed as the "good" side and we have no option of helping the other side.
Personally, I prefer an Oblivion style storyline. I also suspect that that's exactly what we are going to get.
The New Vegas writers wrote themselves into a corner by allowing you to choose sides and achieve multiple endings. But, they had the luxury of doing this because they were bringing the game to a hard end and only had to deal with the results of these multiple paths in a slideshow. Skyrim is an open ended game, so has to reach a predetermined after-story state. This implies that either the civil war is just a backdrop conflict that doesn't actually get resolved during the game or that the winner will be predetermined in which case it doesn't make any sense to be able to 'help' the side that is ultimately scripted to lose.
As to which side is good and bad, that's up in the air. Even if the empire in question is the Mede Empire, it will have been 160 years old by the time the events of Skyrim takes place, if I'm not mistaken. A lot can change in 160 years and by then the Empire may be largely benevolent and a boon to it's peoples. Likewise, rebellions aren't always based on noble ideals nor do they necessarily create a better life for the people when they succeed. Personally, I'm hoping that the Empire is the good guys because the 'Evil Empire crushing freedom fighting rebels' is just a little bit too overdone.