I don't think a genocide argument is a valid one in Skyrim. Certainly, there is victimisation and separatism, but it hasn't flowed over to outright extermination, 'yet'. The Stormcloak leadership has a very simple, very effective, and in terms of our real world, historically precedented, tactic...they offer jarls and cities the opportunity to join them, and if it's refused they wipe it out. Alexander used to do it, the Romans used to do it, and numerous others used to do it. It's not genocide, it's the 'join or die' strategy.
In respect to the 'Thalmor threat', there's too little information on what the situation is across the entire Empire and the strategic balance against the Thalmor to make an accurate assessment. The Thalmor are more or less acting in the role of a superpower, with 'advisors' in place, monitoring things. That leaves them a range of options. The issue for the Empire is that if they strike, they have to strike everywhere at once, to cripple the Thalmor intel and communications, while maintaining a credible defense.