Reading over this entire thread I think that the teacher DID listen to your concerns and placed your son with violin BECAUSE of the self esteem issues.
It would seem to me that since percussion is SO competitive in the higher grades that it could crush a child without much confidence. How would your son feel if he played drums this year and thought he was doing them well and was proud of himself and then did not make the cut nest year? Or the year after? It can be hard even on very confident people to handle the rejection of losing a try out for something you have worked hard for. It could be devastating for your son.
Also, it sounds as if your son's experience is with a drum kit. This is pretty different than orchestral percussion. So right now his drumming skills are something he is proud of, right? What happens when he gets into orchestra and finds out he does not have percussion skills yet and THAT is a struggle? Will his self esteem take a double hit? Meaning he is not only frustrated that he is not picking it up fast enough but he now looses his pride over his drumming skills that he now has.
Finally, as a mother of one very anxious young lady and one young man with processing and motor and speech issues--please try not to borrow trouble. Be excited for and with your son--he got what he wanted.

Maybe struggling to learn an instrument (that his dad does not play so he will not compare himself there either) and seeing the results of his hard work turn out well by year's end will be just the self esteem boost he needs.
EDITED TO ADD: Oops, I forgot to answer your original question. When I was in Jr High my parents had no say in my choice of instrument. I don't think they ever got to meet the teacher--they would have liked to meet him though. If y children's school gets a grant to cover music again I will not expect to have an say OTHER than if it is a large cumbersome instrument it would be an issue because they have to walk a ways and take two forms of public transit to and from school (but then I would try to work out a reasonable deal on renting two or something and have one stay at school and one at home).