That's absolutely true. We're talking about normal distributions that partially overlap. No one is saying that no women want to be programmers. Just that there's less of them that want to be than men.
The point is brain difference issue is a red herring. Based on it we can't conclude what gender split will be exactly and thus can't conclude that other factor does not play deciding role, like culture of blatant misogyny widespread in this young profession, or prevalent stereotypes influencing career choice that don't have sufficient grounding in reality, or economic factors.