Aren't all activities only popular among children who are good at them? From academic study, to music, to sport, to drama…
I'm not sure rugby is of 'questionable safety' – there have been some horrible incidents, granted, but they are high profile precisely because they are thankfully rare. My 2 DCs both represented their schools/clubs at numerous different sports and yet their two most serious injuries came when 1) hit by a body board in Cornwall and 2) when putting a hand out to break a fall on a day much like today which resulted in a complicated spiral fracture. DS suffered more broken bones on a tennis court than he did on a rugby pitch
If you dig down into Dr Pollock's figures you will see that if your DS is not playing for a school team he has less than 10% chance of being injured playing rugby before the age of 17. I'm not saying we should ignore opportunities to make the sport even safer, but a sense of proportion is required.
All that said, Neme, I'm sure if you don't want your DS to play rugby and he has no desire to do so, then the school will at least listen to your concerns. The new head is coming from an all-girls school so possibly he will be amenable to boys being excused rugby.