Girls tend to hit puberty earlier than boys, but AFAIK going through puberty doesn't effect how well a kid understands school material. Even if it did, every child develops at a different rate, so your system wouldn't be any use for a boy who hits puberty at eleven or a girl who hits it at fifteen.

Instead of separating boys and girls because they're awkward around each other, adults should teach kids to recognize that the members of the other gender are just people, and that there's no reason to be nervous around them.