You will need to help your son to understand that after school activities are not evil. If sports are evil, then why do JWs watch them? So it's important to help him to understand that his dad and JWs view them as evil because they fear the bad association and interference with service to Jah, etc. Help him to see that all non-JWs are not bad association and that whether he is involved in after school activities or not he will need to strive to avoid what is really considered to be "bad association".
I agree with your concern and the structured environment. My child loves sports. I've seen good results from his involvment. He currently holds 3.5 gpa in honors classes, but was borderline before with failing grades. The coach requires biweekly progress reports with 2.5 or better and no failing grades in order to play. They sign a contract, no alcohol, no drugs, proper use of social network. He is too tired after practice to go hang out in the streets like he used to. Children get board easily and will find something to get into good or bad. There are at least 8 other JWs attending his school. I try to help him to understand the JW view of sports and that he must have respect and use discretion so as to not rub it in their face but at the same time, this is a personal decision that we have made and that he is not doing anything wrong, as long as he stays out of trouble.
i hope the best for your son and that he's able to decide for himself instead of being intimidated with some imaginary "evil".