J.,
If memory serves me correctly, you had a similar post earlier. Something along the same lines, your boys misbehaving, problems at school, etc... It seems to me you have not gotten this issue under control. You may not be accepting of my advice but here it goes...
You should try to change class for your eldest son. That may help a bit. However, you need to make sure you are doing your part as a parent. By you stepping in when the teacher grabbed him and took him out of line for hitting another kid, you underminded the teacher's authority. The best place to confront this issue was probably in a conference with the teacher, principal and yourself. Your sons (both) know that you take their side. Therefore, they will continue to act up until YOU start to be firm and reinforce the discpline and rules at home that they have to follow at school. In my opinion, I don't think the teacher is being "one-sided", since it seems both your children are having behavior problems. Also, you need to get the teacher's side of the story. Stop being part of the problem and start being part of the solution. Hope this doesn't sound too harsh, as that is not my intention.