As a male ex Rugby Union player, I have to agree with what Jaques says. I think it would be extremely dangerous for boys and girls to play mixed contact Rugby beyond primary school. At that age (and sometimes earlier) boy's muscle density begins to increase and there would be very few girls who could cope physically with this challenge.
How do I know? Mainly because I was a late developer and, although I loved Rugby, I simply couldn't compete with my peers until my mid teens, when I began to 'fill out'. In the three or so years before I grew, I got beaten to a pulp on a regular basis... Fortunately for me, I had some useful skills and stuck with it until I was big enough, but it wasn't until I was over 18 that I began to be selected to play for actual teams.
Perhaps one or two girls could cope and might develop fast enough but I wouldn't want to be the PE teacher responsible...
Women's Rugby, however, is a fantastic sport and I'm happy to watch it whenever the opportunity arises. They don't have the same power as the men but the skills and tactics are amazing, especially when you consider how relatively young a sport women's Rugby is.
As for the OP. When I was at (an all boys) school you had no choice but to play Rugby, there wasn't even a football alternative. The kids who hated Rugby still had to play but they were never teamed against the guys who did want to play - they were sent off to another pitch and quite simply didn't put as little effort into it as they could. If the ball came to them they simply kicked it away or passed it (ie threw it away asap).
I'd suggest this might be your son's best option to avoid the wrath of the PE teacher (and to avoid potential difficulties with his peers). He needs to appear willing but do everything possible to avoid actually taking part: It's not that difficult because at that age Rugby is pretty disorganised, it just requires a bit of imagination. I'd suggest that this approach might be a pretty useful lifeskill...