Actually, it was totally free in terms of the school not having to lay out any cash. The reason we chose to work with them, however, is that they committed a ton of time from teachers, students, administrators, and parents to help us make the Khan Academy work better for the classroom use case.
The experience working with them has been fantastic. The teachers are fearless in the face of the significant uncertainty that introducing something like the KA in a classroom can create. They've been creative about experimenting with different ways of integrating KA into the classroom (trying things we didn't anticipate). Speaking as a UX designer, having nearly unlimited access to teachers and students for interviews and observations has been invaluable. Plus the teachers aren't shy about letting us know if something isn't working out. If anything, it feels like we should be paying them.