We have a 14 year old daughter who also attends Christian school. In the 6th grade, I found the environment was not conducive to what I wanted for her in terms of student quality at her then Christian school. Many of the kids were mean and inconsiderate of each other. Despite this, and going back in forth with whether she wanted to stay or leave, at the end of the year, she did not want to move or change schools either.
I switched her to a new Christian school the next school year. Beforehand, I talked to her about the problems she was having and that I did not see these things changing. I reminded her of the roller coaster she was in there as well.
While I try to listen to my children and support them, I do not solely trust the judgment or maturity of a then 12 year old when it comes to major decisions. Getting a quality education is just as important as our children's development; who are they becoming.
I was not as concerned with the academics at the new school as the curriculum was similar and this was Middle School. I am a teacher by nature and a stay-at-home mom who stays on my kids and their grades.
I made the decision and have not regretted it. Yes, she had to make new friends, but as parents, we are given the charge of doing what we feel is in the best interest of our kids, even if they do not agree with those decisions. I told her that if these kids are meant to be her friends, they will remain in her life. She still talks to some of her friends at her old school and they hang out from time to time.
Our situation was the flip side of your coin. The academics was good at her old school, but the environment was not. I had observed her picking up traits which did not line up with what I wanted for her or what I felt was healthy or positive for her developmental growth.
That being said, is it possible to talk to a couple of parents or students at the new school to get a better idea of the academics. Sometimes the grass is not always as green as we might hope it is. Also, go to www.greatschool.net to check for parent and student reviews of the school you are considering.
Bottom line; do what you think is best for your son. Change is a part of life. If you decide to make the move, show him the benefits of these changes and reassure him that he will be fine. You have to see the big picture, and if you discern or suspect something is wrong and something needs to be done about it, then it's on you to do it.