The Mind Control Center does restrict how easily planets flip, even though it was supposed to make it easier - I think they changed the description so it doesn't say that anymore. Either way, it's annoying.

Your best bet is to build your reeducation center on that planet (to prevent it from flipping back to you) and then sell the planet to someone else (preferably an ally so you won't go to war with them). Selling to a minor civ works, and you don't need the reducation center. If all else fails, you can destroy the colony.

Tell me about it. I play a very influence-heavy custom evil race. Winning without the MCC adds at least a year onto every game - although now that I'm used to it, I don't know what I'd do with that much extra money.