This is a problem for schools using usually custom-built tools to manage the district's resources and administration. For the more flexible charter schools that are more open to the idea of adopting something like Khan Academy into the curriculum, they are small enough (usually one school) to switch over, and are often already using Google Apps as their default method of email and collaboration.

I know that at my sisters' charter school (2 schools, K-8 and 9-12), the entire school is on the Google Apps Education platform and getting started with Khan Academy was really simple for them, as they already had name@school.com email accounts they were used to using.