You take out some corrupt people in the questline, including some higher-end ones. You could view the other contracts as a means to an end if your character is a pragmatist. That or you could use it merely as a place to train and hone your skills, without actually taking on any contracts.
Well I'm a Stormcloak at heart, but I'll have to say neither. They're both revealed to have been guilty of atrocities, and their morals and motivations are subjective. My character does as much as she can to impede them both.
The current Emperor condemned the free will of the people by agreeing to the White-Gold Concordat. Nobody should be told what Gods they can or can't worship. Also, as you said, there are some corrupt people killed such as Grelog the Kind at the very start. The rest are, unfortunately, just a means to an end. My guy will need the backing of the Dark Brotherhood to become a successful assassin. Plus, at the end, when you
Spoiler become the leader of the DB it could be that my guy is trying to change their ways to only kill the bad from an RP point of view
.
As for the war, I will keep my guy neutral for as long as possible. But, once I begin to run out of other quests, I may have him side with the Imperials. Whilst they are far from perfect, a long war only leads to more casualties. Plus, my guy would not support the racist views of some of the Stormcloaks nor want Skyrim to be at risk from invasion from the Thalmor as they prevent people's basic rights such as religious believes.
Now, what reason could my guy have for visiting Skyrim? I don't know much about the Breton race...