I like to call it the tower theory, anyway. It's the belief that certain stones/items/places of power (towers) across Tamriel stabilize Mundus, and also that the Thalmor are trying to destroy the remaining towers.

For Tower Theory: The Thalmor started the Great War to control the Empire, thus controlling the worship of Talos. They ban Talos worship to destroy the divinity of Talos in Aetherius by destroying his divinity in Mundus. They also plan Skyrim's civil war from the start, by instilling hatred for the Thalmor in Ulfric and releasing him from their custody as their pawn. They also take advantage of the Markarth Incident, forcing Ulfric to rebel further. By starting and keeping the civil war going, the Snow Tower is destroyed, and they are one step closer to their ultimate goal of unmaking Mundus and returning to a spiritual state.

Against Tower Theory: The Thalmor startted the Great War out of fanatical hatred of the races of men, and so they take man's Empire, and the symbol of that empire, Talos. They capture and release Ulfric to cause a civil war in Skyrim, which either way would weaken the Empire. They don't strictly outlaw Talos worship until the Markarth incident, a chance occurrence, and so are not consistent in their plans to ban Talos worship. You may notice it makes no sense for the Thalmor to actually believe in the Eight Divines. The ban is strictly propaganda against a man becoming a god. They already believe their ancestors, and they themselves in a sense, are gods. If they were serious about banning Talos worship, they wouldn't risk allowing the Stormcloaks to win, since they already control the Empire. But by allowing the civil war to continue, both sides are weakened in the end. If the Empire wins, it's more vulnerable to their next attack. If the Stormcloaks win, the Thalmor can wage war with Skyrim without having to worry about the Empire getting involved, and then they'll have one more territory.

I can see how you can view it either way. I welcome any facts for either viewpoint I may have missed or misinterpreted.

In the short term, they don't need to bring down the towers to bring about their goals, and the Civil War weakens both Talos and the Empire, making it that much easier for them to wipe them out later. Remember, the Altmer live for centuries. They're playing chess while the Nords are playing Cowboys and Indians, not realizing that it's in fact the same game.

Also, you shouldn't try to apply real-world religious logic to TES. In Tamriel, all religions are true and all gods are real, and are acknowledged as such by every mortal race. The Altmer may hate Talos, but they can't deny his divinity. Which is why they must strip it from him.

But they can't, can they? I've been told that Talos cannot be removed from divinity due to his achieval of CHIM. However, I've always wondered what would happen if the Thalmor were able to remove Lorkhan from history. If Lorkhan ceased to exist, how could any of the three-as-Talos mantle him?