I think you're misunderstanding the Khan Academy model. I saw a video where Sal said that in a traditional model the time it takes to learn something is fixed and the quality of what you learned is variable, whereas in the Khan Academy model the quality of what you learned is fixed and the time you take to learn it is variable.

Essentially, under this model everyone is expected to eventually master the material--so in many ways this is harsher than traditional grading. It would be equivalent to him taking calculus until he got an A--not just taking it until he managed to pass.