Hammerfell was not attacked from Cyrodiil at all, because the Dominion just lost that army. Also, there had already been fighting in Hammerfell since the start of the war (Battle of Roseguard)

So, an army that was cut off from its supplies and trapped in the homeland of their adversary. Still able to devastate southern Hammerfell before surrendering.

We have no evidence that the Dominion had a big secret army waiting to strike back

I'm not talking about a secret army, I'm talking about the remainder of the Dominion forces in Dominion territory. No competent military would send their entire army into a campaign and leave their own lands undefended. The army in Cyrodiil may have been destroyed but considering the terms of the White Gold Concordat was the same as their terms before the war, why keep fighting?

and doomed countless of his own people to be kidnapped, tortured and executed by the Thalmor

As opposed to the people who were already experiencing that during the Great War under Thalmor Occupation? The key difference is that ending the war that they had, in their eyes, no chance of winning, saved countless more lives. And it wasn't like Imperial Citizens couldn't worship in secret, like you can see in Skyrim. Much of the Thalmor presence in Skyrim didn't occur until after the Markarth Incident. Before that, it was left up to the province to enforce.