The biggest con for me is that after the imperials move into a hold you've just taken, the thalmor death squads move in as well. You are basicly spreading their grip.
Every Thalmor condition for peace had been an arrow in the body of the Empire. The cession of land was to alienate Hammerfell, whilst the Talos ban was to alienate Skyrim, and their plans worked perfectly, the Empire was forced to abandon Hammerfell when they refused to give up part of their land to the Thalmor, and Ulfric's opportunists took advantage of the understandable agitation in Skyrim to launch a rebellion in hopes of also removing Skyrim from the Empire. It's a classic case of divide and conquer, to soften the Empire up for the next great war. So by defeating the Stormcloaks you are sticking it to the Thalmor and refusing to be used by them.
Besides.. as a faithful Imperial citizen I slaughter all Thalmor on sight. They can be forced to brand me as a criminal, but i serve the Empire and its people and doing so requires sacrificed.
I would say it as "The Thalmor wins either way".
Quite possibly, even if the revolt in Skyrim is suppressed the Empire would have killed many skilled warriors who had been misled to join Ulfric who in turn killed just as many loyalists. Nothing good is coming out of this, while the Thalmor get nothing but gain. Either Skyrim secedes from the Empire, thus weakening the Empire immeasurably, or the Empire suppresses the rebellion and loses a legion in the process. Even if Imperial loses are low, the physiological divide in Skyrim would prevent a truly unified front against the Thalmor next time.