I was able to get a response back from Wizards of the Coast. They can't give me a complete response on legal issues, but:

"We like where DDO has been going lately and hope it continues to flourish."

So it looks like, if Atari does lose its licensing agreement, then at least Turbine won't have much of an issue simply running their license directly through Hasbro. Of all the reasons for an MMO to shut down, losing their license would be the worst.