Did the empire conquer skyrim or not ? how did they come to be there in the first place ?. The romans allowed Gauls to join its military yet the Gauls staged numerous rebellions non of which is ever referred to as a civil war. When the natives of an occupied province rise up against the occupiers its a rebellion thats not the same thing as a civil war.
Skyrim is not under Imperial occupation.
1) As I read http://elderscrolls.wikia.com/wiki/Tiber_Septim, the Empire did not conquer Skyrim. Rather, it was much the other way around: Tiber Septim marched into what is now Cyrodiil under the banner of Cuhlecain, king of Falkreath, and established the Empire. If anyone was occupied territory, it was Cuhlecain's/Septim's Nord and Breton forces occupying the Imperial heartlands, not Nord territory being occupied by Imperials.
2) Even if the Nords had been brought into the Empire through occupation, the Empire was formed (with the Nords a part of it from the start) at the dawn of the Third Era.
Oblivion took place (and ended the Third Era) in 3E 433 and
Skyrim is set in 4E 200. That's 633 years of Skyrim being a willing, peaceful member of the Empire with no evidence of subjugation by Imperial forces. Calling it "occupied territory" by virtue of Imperial conquest after that long, even if it had originally been brought into the Empire as conquered territory (which, again, it wasn't), seems unreasonable. If Skyrim is still "occupied territory" after six centuries, then most of Europe must also be "occupied territory" today, owing to having been captured in medieval- and renaissance-era wars.