'Holes' wasn't actually made by Disney. It was made by Walden Media - an new company that was founded by an educator and two former Miramax executives. They also produced 'Ghosts of the Abyss', the 3-D IMAX documentary about the 'Titanic'.
They have big plans to become a major producer of both family entertainment, a producer of family theatrical shows and of educational media. I believe they have already opened up a theater for family plays (in either Utah or Colorado) and plan to offer touring companies as well. I think their next big movie is a remake of 'Around the World in 80 Days' starring Jackie Chan. They are also producing 'The Lion, The Witch and the Wardrode' as an animated feature.
Disney's responsibility is to book 'Holes' into theaters and advertise the film, but they had little control over the actual making of the movie. I do not know the exact financial terms of their deal with Disney, but creativity it likely works similar to the Pixar deal: Disney stays out of the production process.