Stopping them as a united Tamreil is way more important than worrying about Talos's temporary weakening or whatever.
The Empire was already a united Tamriel and the Aldmeri
1. Defeated the Empire
2. Controlled them
Literally
the Thalmor will actually leave Skyrim if the Stormcloaks win the civil war lol. They could only maintain a hold over Skyrim via Imperial influence. Hence why the Thalmor outwardly support the Empire winning the war.
Also Hammerfell is independent and the Thalmor can’t do shit to Hammerfell lol. Hammerfell and and Independent Skyrim would ally in a mutual desire to not be controlled by the Thalmor.
Also, the Dragonborn is so powerful that whatever the Dragonborn wants to happen will happen. If the Dragonborn tells the Thalmor to bend over and get fucked, they will ask how hard or die lol.