I am actually of the same mind as you, Maelora. In my campaigns, the Rebels are the good guys, and the Empire are the bad guys. But what makes the game more interesting, engaging, and realistic is to point out that not all Imperials are bad, and not all Rebels are good. Moral grey is abundant across the galaxy.
Oh, definitely. I'm having an Imperial civil war, and one of the faction leaders is the fairly reasonable Wulff Yularen.
At the same time, there's a rival cell for the PCs, a 'Bad Company' cell that basically carries out terrorist acts against anyone even remotely connected to the Empire. Some of them have sympathetic backstories, but they are certainly giving the Alliance a bad name and end up helping the Empire's propaganda. And the top brass haven't done anything about them yet because sometimes, they need operatives to get their hands dirty...
The players are definitely the good guys, and that should be hard. It takes moral fortitude and guts to do the right thing when other people around you are taking shortcuts. The Dark Side is quicker and easier, and more seductive... but ultimately comes around to bite you on the ass.
Edited by Maelora