Ancient Romans threw and executed Christians by either crucifying them or putting them up against lions in the Coliseum. This made Christians grow closer to that religion. Still nothing really changed despite Christianity is widely worshiped and followed. Now despite all of this, people will claim this has nothing to do with a fictional game, but they are good examples and are only such.
Just like in Skyrim, this is what we are witnessing. The Nord's and everyone else are rejecting the Thalmor ways and people are secretly worshiping Talos any way. The fact that the Thalmor is trying to get people to abandon their religion is only making those people do it more and become closer with Talos.
I doubt the Empire will continue to tolerate the White-Gold Concordat for much longer.
The Thalmor are on a self destructive path and this is doomed to fail. So Not much will really change. It really depends if Bethesda wants it too though, but I doubt it .
The eradication of Talos is they're current M.O, and replacing the human variations of the divines with the Aldmeri ones is...unlikely. I doubt they'll go anywhere near the lengths the Alessian Order did in eradicating human aspects out of the divines like they did the elven, at any rate. They might see it as backwards, but they're not gunning for Akatosh or anything else as of now.