The Thalmor are there 'to help quell the rebellion'. No rebellion, no need or justification for a significant Thalmor presence. Imperial troops can keep their attention on making sure the Thalmor don't exceed their mandate. Prepare for war, worship in secret, stand a chance in the next war.

Instead Ulfric provides the civil war based on the outlawed religion that they need as a legal excuse for the Thalmor to run amok, and ensures that Imperial troops can't legally do anything to keep the Thalmor in check. That's the breaks, and of such breaks is history made.

No, they're explicitly not there for that reason*. It isn't stated anywhere in the game, as far as I know, that they in any official capacity is there under such pretenses. They are there, officially, to make sure that the Talos Ban is maintained and to hunt whatever Blade members are hiding in Skyrim.

*I quote Emissary Elenwen( http://cs.uesp.net/index.php?game=sr&formid=0x000e16f4 ):

As long as the Empire continues to uphold its treaty obligations, my government does not concern itself with the internal politics of Skyrim.

And she says this during the Diplomatic Immunity quest:

"The Thalmor Justiciars are so often misunderstood. Our primary goal is to preserve the peace between the Empire and the Aldmeri Dominion. The worship of the false god Talos contributed to the unfortunate friction that led to the Great War. Following the Great War, the White-Gold Concordat set out the terms for peaceful coexistence between the two powers. The Empire and the Dominion agreed that the worship of Talos was a relic of the past, and must be eliminated in the interests of peace. But I'm sure you didn't come here for a lecture on high politics."

And Ondolemar( http://cs.uesp.net/index.php?game=sr&formid=0x00064788 ):

I was sent here to lead the Thalmor's interests in this corner of Skyrim. It's my mission to root out all Talos worship in this city

Your assertion that the rebellion is the cause of the Thalmor presence is fundamentally and demonstrably wrong, discredited by the Thalmor themselves.

Nostalgia, loyalty, suspicion of Ulfric's motives, family legacy, believing in "the dream," personal admiration of Titus Mede II and/or legion officers.

And the Thalmor never exaggerate anything, amirite?

And since the Empire clearly isn't upholding it's treaty obligations we're here to help. The fact that our agent is the reason the Empire can't uphold its obligations is certainly convenient for us, isn't it?

*I quote Emissary Elenwen( http://cs.uesp.net/index.php?game=sr&formid=0x000e16f4 ):

As long as the Empire continues to uphold its treaty obligations, my government does not concern itself with the internal politics of Skyrim.

But since our agent has made that impossible for the Empire here we are, and the treaty forces you to allow us to operate freely since you clearly can't uphold your part of the deal.

Bottom line, the treaty cuts both ways. If Skyrim was at peace and not full of wild eyed Talos worshipers publicly flaunting the law the Empire could pressure the Thalmor to back off...but it isn't at peace and it is full of lawbreakers, so the Thalmor are not going away.

Prepare for the next Elven war, quietly worshiping whoever you want in your own homes...men have a chance. Squander resources on a civil war, elves win the next war hands down. If I hadn't disliked the Altmer all the way from Morrowind on I'd probably side with them out of respect for their cleverness.

But as I said this is the view from outside the game. In the game I can play a character on either side of the civil war.