The Imperials are just making best of a bad situation. In fact, it was pointed out (by Rikke, I believe) that nobody was even being punished for worshiping Talos in Skyrim until Ulfric got his panties in a bunch. Also, remember, the Empire was STARTED by a Nord, so being against them just because you're a Nord/from Skyrim doesn't really apply. And, honestly, does it really seem like a good idea to break up the provinces of men? They couldn't beat the Thalmor when they were united. What makes anyone think dividing up the Empire into even more groups will be beneficial to their long-term survival? Quite frankly, to me, from a socio-political viewpoint, siding with the Stormcloaks seems like it's just a bad decision, unless you want the Thalmor to win (in fact, I'd imagine the Thalmor want the Stormcloaks to win so they can swoop in and take over...it'll just lead to a repeat of the pre-Alessian slavery of men).