Hi J.,
I was very similar to your son when I was his age. I gave up sports and became a "skate betty". I withdrew from my family and I did begin to hang out with the wrong crowd.
During my adolescence my mother faced many medical/health problems and was "absent" from my life. What I was truly wanting deep down inside was structure. I wanted my mom to tell me to be home for dinner and what time my curfew was. But she didn't so I stayed out late with my friends and learned the hard way.
I think it's important you allow your son to ride his skateboard, but also keep him engaged in a team sport. Team sports make him responsible and accountable to others. His team needs him and he is obligated to be there for the team. And yes, twelve year olds want to start making their own decisons, but the truth is - they are still children and you need to be the parent. I don't believe he is old enough to make those types of decisions on his own and as his parent you know what is best for him. You know your son. Keep him engaged - be involved - don't let him pull away because he will need you more now as he grows through adolescence than you can ever imagine.
I know I needed my mom and because she allowed me to make my own decisions, I failed. Luckily she refocused her energy on me and it took her a year to straighten me out. I have forever been grateful she caught me when I fell and I am now 36 with my own two children (one to be 12 on the 30th of this month).
You're a good mom and remember, it is in our nature to protect our children. Keep doing so and he will thank you later.