I guess it's because you can be on the side of the Empire and still be someone good. I play an Imperial agent and yes, you do bad things for the Empire (you kill rebel slaves, etc) buuuut you can still think it's for a greater purpose: for order and security, while rebels are terrorists, etc.
You can be a very bad guy and full dark side sith, but you can also be a loyal Imperial agent who think he's doing his job for a good reason.
It depends on how you play, really. It's interesting to have a character working for a villain like a Sith but still struggling to make good actions. And a lot of Imperials don't like the cruel ways of the Sith, so all of them are not bad people.
I think thats whats more or less endeared me towards the Empire and more specifically the IA class. I always preventing the the death of innocents and refrained from executing people who didn't really deserve it. I mean in Balamorra for example (minor spoilers)
.its fantastic that game could give you such mixed emotions.
Whereas on the Republic side you were more or less expected to be a good, merciful guy and even when you went Dark side it just made you look like an irrational jerk instead of someone doing all thats necessary to achieve a utopian goal.