The biggest attraction Marvel Comics has for Disney is its media entertainment branch. That's largely it. Disney financed both Narnia films, when they compared how much they made with those two films to what Wolerine: Origins or Iron Man made at the box office, they probably thought "oh shit." With the plethora of films Marvel is currently developing and acquiring financial resources to make those films, it made sense for both parties to come to this arrangement.
I'll be willing to flat-out say that unless the Disney brand appears on the cover a Marvel comic book, they won't be concerned at all with dictating the aesthetics of how Marvel publishes their books. In the end, its all about making money for the boys up-stairs [as far as Marvel Comics publishing is concerned] by continuing to make and release comics for the adult hardcores, and why mess up a good thing?