There is a slim chance, but the issue here is not really the Groening thing. If anything, I would have thought it would work in his favour. FOX would want to get back on his good side, for future projects and maintaining a good relationship on The Simpsons.
The more important matter is cash. Family Guy doesn't have any of the 3D stuff of Futurama, and in general just seems a "cheaper" sort of animation than Futurama. As mArc pointed out, a "Flash" style of animation for the show wouldn't be as difficult to sell as for Futurama.
So, while I believe that yes, there is a slim chance for Futurama to get a movie, I'm not going to hold my breath. As far as I'm concerned, we got at least 4 seasons of pretty good show. Anything further would be an amazing bonus.
I'd also like to add that a full-length Futurama episode would fit so much better than a Family Guy one.