Oh no I totally agree with you. It's embarrassaing enough and w/ boys it's 100% times more.
I had definitely wished we were in seperate classes, (In 5th grade when we learned about periods we were) but in high school we weren't. Same thing in gym, that was also bad, probably worse becasue I got mauled down all the time and wouldn't even participate then.
It would definitely allow for better discussions, becasue the sexes wouldn't be so afraid to ask questions about their body, believe me they were. Honestly I hated it when I was in health becasue it's so uncomfortable and only appretiated the knowledge in college, when I put it to use. I guess it depends when you put it to use. It would be so easy to seperate the two, and I think some schools may, but mine was definitely into the whole "progressive" thought that all boys and girls will be the same, and the truth is we're just not.