At risk of invoking Godwin's Law, such arguments didn't work out so good for Albert Speer, Rudolph Hess, Karl Dönitz, et al. The job of the state is to administer justice and protect its citizens, and being subject to orders doesn't give you a pass on that duty. Does being sworn to obey the Emperor put him in a difficult position? Yes. Does that mean what he's doing is just? No it does not. The position that you can oppress a minority for the sake of civic order is NOT defensible, period.

And the suggestion that delaying the oncoming conflict with the Thalmor plays in favour of the Empire is patently false. The Altmeri Dominion is internally united under the White-Gold Concordat, and the Empire is fragmenting, with both Skyrim and Hammerfell rebelling under the yoke of Imperial tyranny. What sane leader would try to throw off the yoke of foreign aggression AFTER fighting a grueling civil war to enforce the terms of their last treaty? It's dilatory appeasement and serves only to strengthen the Empire's enemies while weakening itself.