[quote=Blitzkrieg]
The Thalmor have used more complicated means to advance their own goals.
[/quote]

They use those sorts of strategies in the struggle for control of the Tamriel, yes, but the thing about Talos is less a struggle and more a policy that they are enforcing on everyone under their control. I think there was something about them murdering children in Talos worshiping families because they were corrupt (But that might have been from 3dnpc), so I don't think they would let a guy who is constantly disrespecting their control live off of some scheme that he is doing more harm than good.

Really there are a lot of open Talos worshippers in Whiterun. It makes some sense for them to be there when Balgruuf isn't allied with the Empire, but after he has submitted and after the war is over it doesn't make much sense that the Thalmor wouldn't have a presence in the city and thus a lot of the people would be dying, but really that could be said about all major stormcloak cities. It was deemed an acceptable plot hole, obviously, they didn't put much work at all into the war questline so clearly they aren't about to make major changes to the world just because it is completed.