Either way, the Thalmor-Empire war is inevitable. The former's goals include the genocide of the human race, from what I've read. The treaty is just a temporary ceasefire for both sides of the conflict, giving each side time to build it's strength up.
Of course, that's just me speculating based on the bits and pieces of the story we know.

1) The Empire has absolutely no clue what the Thalmor is up to. They let them murder all the Talos worshipers because "hey, what's the worst that could happen?" They will get completely blindsided when the Thalmor move, again.
2) The Empire does know what the Thalmor is up to. They let them murder all Talos worshipers because Mede is an idiot and hoped to be saved for last. And they will never be a threat again.
Either way, the Empire will never be stronger. They are crumbling.



)
Time to secede.