Why is an explanation required? Any developer worth his or her salt knows that, statistically, something like this is bound to happen over enough companies and enough years, even if the trend is so heavily skewed the other way.
Is this a 3 sigma deviation? Maybe. Or could it be that, on average, women might be drawn to educational software more than other types? Doesn't sound unreasonable.
Regardless, your insistence on an explanation shows that you're still stuck in the bad old days.
I'm pretty sure most universities have a company mission that appeals to both men and women and they haven't suddenly seen a 2:1 f/m ratio in CS majors. What makes Khan so different?
He might have a point in that a lot of women seem to aspire to be teachers. For example when I got my maths degree, 99% (estimated) of the women sitting in the lectures with me were studying to become teachers. Perhaps working for Khan Academy somehow seems close enough to teaching.