No it's a rebellion against the occupation force. There are Nords fighting on both sides but it doesn't make it civil war. The ones on the side of Empire are traitorous ones who have betrayed their own people.
Skyrim is part of the Empire though, so that argument is invalid.
Thats like saying the US civil war wasnt as a civil war because the South was occupied by a foreign force, the North. Obviously thats going to be the viewpoint of the guys trying to secede, just like the ones trying to keep the country together will say that the other side are merely rebels against the legitimate autority, that no one should recognize them, and that crushing them is purely an internal matter, refusing to call it a civil war for these reasons.
Essentially, civil war is the neutral term, which neither side truly likes (because it doesn't put THEIR side ahead) but that is fairest and most neutral to describe a conflict.
In Skyrim, the rebels cry Oppression and the status quo forces cry Aggression. But the truth is that the most balanced term to view the conflict is 'Civil War'.