Here's the problem though: if you're interested in meritocracy, it has to be a true meritocracy all the way through. You can't ignore other parts of the process and then, only at the very end, say that the quality of work is the only thing that matters. Sure, if boys and girls at home and in our education system were treated equally, encouraged to pursue the same things, given the same opportunities...then yes, you could make this argument.
The problem, though, is that this isn't the case. Women in the United States aren't shying away from STEM disciplines because they're generally intellectually incapable of it; it's because they encounter strong societal pressures against doing so. Other countries--I'm thinking of Romania in particular, which sent a large number of IMO medalists to my university during my years there--have many more women in math and science. (And no, they're not bad at what they do.) Unless you're going to try to claim that Romanian women are somehow different or more talented than American women, it seems clear that the ways that our society and educators are affecting them are responsible for this disparity.
And once you take that into consideration, the argument for improving this problem starts to become a lot more reasonable. It bears a lot of similarity to that line from Lyndon Johnson: " You do not take a person who, for years, has been hobbled by chains and liberate him, bring him up to the starting line of a race and then say, 'you are free to compete with all the others,' and still justly believe that you have been completely fair."
It's pretty similar here. Jean (and others dedicated to this cause) aren't interested in "skewing" the game unfairly. Instead, they contend that because of issues earlier in the process, whatever they may be, the gender gap isn't and shouldn't be the natural order of things.