I have been using Khan Academy in the classroom for the past 6 years. I believe student buy in is a must. I do this by offering small rewards for increasing their score by 10,000 points or by going up in percentage on the mission they are working on in class. Rewards are usually in the form of candy or stickers.
I also encourage students to work on the mission in previous courses (when they have free time). This is a great way for students to review skills and also earn more points.