It seems to me that by cooperating with schools and introducing assessment, Khan risks losing his way. The educational value will not be improved by becoming more schoolish -- schools are the problem.
As hackers know and as Mitra showed, learning is fun. However it ceases to be fun when one is told what to study and pressured to compete for meaningless grades/scores/badges.
(IIRC, Mitra doesn't assess children directly in the sense of giving them grades.)
Also, now that Khan knows that children will be assessed on his video material, I expect that this will skew his future presentations in a bad way.
Mitra has developed and proven a methodology for teaching children in-person using small groups and computers.
Mitra + Khan makes me jump out of my seat.
Here is an incredible introduction to Mitra's work : http://www.ted.com/talks/sugata_mitra_the_child_driven_educa...