Disney is in the process of setting up a digital animation facility whose first project is supposed to by Toy Story 3. This will certainly throw a monkey wrench into the current negotiations to extend the relationship between Disney and Pixar, since Pixar is opposed to the idea of a third movie.
Unfortunately for Pixar, Disney owns the rights to Toy Story.
Unfortunately for Disney, I doubt they'll be able to make a third film worthy of following the previous two without Pixar.
Come on now, Disney... Toy Story without Pixar at the reins? Hellooooooo....?