It's no different than the Nords who were killed because they sided with the Empire. The Stormcloaks come in, and beat up on the Empire, along with the Nords who support them. Do you understand now? I should hope so.
No its different. The thalmor were fighting to gain ownership of Valenwood, and had allies from inside, while the empire was fighting to keep Skyrim in the empire while they had allies from the inside. Key differences is that Skyrim still belongs to Nords, always was a part of the Empire when the Empire was formed, so it wasn't a takeover, and Valenwood is completely ruled by Thalmor.
Hey Nords! Do you guys still rule your land? Nord: Yip.
Dunmer? You? Dunmer: Argonians try taking it, but yip.
Bosmer? Bosmer: Well half of us sided with the Thalmor... Hows that going for you? Bosmer: ...... we have purges now....
