I think it's a glitch, I haven't had it happen, but then I only cleared out the one near Whiterun.

I think it's pretty clear that even if substantial amounts of the Altmer on the Summerset Isles are not in favor of the Thalmor, the Thalmor certainly control the territory and ruthlessly purge anyone who is opposed.The Dominion still needed manpower to prosecute a war against the Empire, so they certainly had effective majority support.