Part of the contract was it didn't effect their next five movies including the Avengers, Thor, Ironman and two others.
I see no reason to assume Disney will interfere with the movies or comics as they, apparently, aren't disbanding or restructuring marvel studios.
Disney has made some amazing, adult, movies in the past, I wouldn't worry about anything yet. Plus, a pixar Silver Surfer would be cool.
Credit to ThaMuffinMan