Sorry to hear your son has hurt himself but it could have happened in many, many different ways, I don't think you are right to blame Free Running. If I had kids I would be actively encouraging them to take it up!
The Free Runners emphaisize the importance of learning basic skills thoughly in a controlled way before tackling bigger obstacles, maybe you should talk to your son about what he is doing and see if he is tackling moves that are too much for him at his stage. There are workshops held around the country where he could be coached by professionals, including many of the heroes of the sport.
Free Runners have a philosphy that goes hand in hand with it about facing up to your fears and tackling obstacles in your way (generally in life) with determination and creativity which I think is very healthy, as is their emphaisis on looking after your body by eating correctly etc. and avoiding injuries which I think is good for any young person. I would much prefer that the younger generation look up to the master Free Runners than relatively talentless singers glorifing gang culture, drugs and guns.