Disney is a big studio like WB, but recently it has not done well, movies like - Chronicles of Narnia :Prince Caspian, Prince Of Persia, Mars needs Moms, John Carter all were big budget movies that failed at Box Office, besides Marvel and Pixar they have not much going in their favor right now.
Hopefully, Alan Horn can give some freedom to new directors and try out some new ideas as he is known to give more freedom to directors to create their project.
As far as Marvel Studios is concerned, it is an independent unit of Disney and it will be allowed to function like that unless it starts making huge losses.