JS doesn't sound like a wise choice to me.
I'd say stick with something a bit simpler, especially given that it's Khan Academy, not Stanford, so it's likely to attract far more casual lay-users who just want to know "a little bit about programming." The casual nature of the engagement means there is probably a very low threshold for quitting if the program is resulting in more confusion/frustration than "aha moments."
I think it's great they're doing it, tho! More people should learn "a little bit about programming."
In fact, it may be what holds us back from genuinely better paradigms.