You have to get to the Empire First to get to the thalmor. By your logic your saying that Ulfric, on his own could raise an army from within the Empire for his own purpose... that wouldn't be allowed. Him declaring indepenence in Skyrim is completley nessecary.
You might have to fight the Empire first. MIGHT. It's far from a sure thing. Hammerfell seemed to have been let go rather than fought for. Certainly if all of Skyrim decided to reject the Empire, they'd probably not fight for it, given how thinly stretched Imperial forces are. Instead Ulfric didn't even bother trying to have a united Skyrim and went straight for having civil war in Skyrim, which is the move of an idiot.
And yeah, a resistance movement can exist within a given government or nation. It could move more freely throughout the Empire than an actual army, and possibly wreck far more harm. Over time the Altmeri Dominion could well decide the Thalmor's goals aren't worth the trouble. It's an effective strategy. This would fairly effectively avoid conflicts with friendlies. Remember, if you end the ability of the Thalmor to maintain any sort of military presence in the Empire, then you end the ability of them to enforce the insane demands of their treaty (which is the only reason it is enforced).
Ulfric had options that didn't require civil war in Skyrim. He didn't even try any of them out, not even the easiest, which was simply talking to the High King before challenging him.