I think that you have to change the text files to remove MEE effects.
In the settings.txt, just set the mega-evil empire to insanely high amounts.
Add a zero to the end of each MEE setting, and you won't have to worry about forgetting what the originals were.
You can turn it off without changing the values. There's a line in Settings.txt that says "AI Uses Mega Evil Empire := True"; just change that to False.
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Cap'n Q
"Good morning, Pooh Bear," said Eeyore gloomily. "If it is a good morning," he said. "Which I doubt," said he.