Which has happened countless times in real history when a war "ends." not everyone surrenders
That's not really the case here
1. The Empire threw out Hammerfell not because Hammerfell particularly didn't want to surrender (remember, on paper this was a treaty, not a surrender, basically a cease-fire), but because Hammerfell didn't agree to the treaty and so to get the treaty with the Aldmeri, the Empire had to throw them out.
2. Hammerfell continued fighting and was successful at knocking down the Aldmeri a peg or two. There is nothing that suggests Hammerfell is weak right now, rather that the Aldmeri suffered considerably at the hands of the Redguard and are the ones weakened -- if there was a time for a counterattack against the Aldmeri it would be now, but the Empire is too afraid and weak to attack.
either way, Morrowind is just going to be a bloodbath and many dark elves will die (well, those that managed to stay alive so far), so the Empire can't get strength from there. Hammerfell is going to get more militarized, and probably have some sort of alliance, if not with all of High Rock, the Orcs. Depending on how Skyrim plays out, the Empire may lose that too. Waiting isn't the solution for the Empire, as waiting isn't going to improve their odds of a counterattack. Hammerfell had it right, and it shows in their successful ability to throw out the Aldmeri.
The Empire also needs to realize most of the Bosmer want nothing to do with the Aldmeri (the coup the Aldmeri used to take over Valenwood hurt the Bosmer a lot too), and could be a great insurgent ally against them. If they can get proof that the Aldmeri had nothing to do with the moons returning, then the Khajiit will be angered that they were lied to and turn against the Aldmeri. That would leave the Aldmeri all alone and bringing the full force of the man races against them would easily squash them.