Actually someone posted the agreement with universal in another thread and it states on page 9 or 10 that 2 years after completion of the land parks east of the MS CAN use characters or character families not used in attractions at universal. So technically that would only eliminate X-Men, The Avengers (Could be argued only Hulk), Spiderman, and the Fantastic 4 as according to it they need to be actual attractions not just have a loose reference to the characters. So there are still Marvel characters they can use for attractions although I'm not sure that Ghost Rider, Blade, or other similar characters fit in at Disney, even at Hollywood Studios.
That said I believe it's already been stated due to a Marvel leak that it has something to do with park concepts in Marvel Comics not the other way around.