My 11 year old son also was told he has hypermobile joints. The Orthopedist recommended he work on strengthening his muscles if he intends to join any sports.
I wouldn’t ignore what the physician told you. Work with coming to a compromise if you can. Stronger muscles do help to support the joints. Maybe combined a gentler form of yoga. You could also get a second medical opinion to see if the physicans concur. Just my $.02.