I quite favor the idea of gender-segregated schooling, because I do think boys as a whole get the short-end of the stick in K-6 because the school environment isn't structured as well for them.
That said, the structure of schooling isn't arbitrary. It's a reflection of the needs of a modern knowledge economy. It's something that doesn't just affect boys versus girls, but certain kinds of boys versus other kinds of boys. Compare your stereotypical programmer to the stereotypical kid who bullied him in 5th grade. More likely than not, the bully had less patience and a lower attention span, more physical strength and greater size, and a well-developed ability to get others to follow him through a mixture of coercion and manipulation. A thousand years ago, at least in Europe, these skills would have been a ticket to higher social status through violence and war. The programmer stereotype, if he was lucky, might have found reprieve in a monastery or something. Of course the shoe is quite on the other foot today, isn't it? The ability to do tedious, boring work for long hours is now valuable, and is basically what modern K-12 education prepares you to do.
Is our modern economy unfair to the bully?