It has been over year since I picked up my younger son from the after school program and told him he was not coming back. In a nutshell, A was engaging in inappropriate social behavior (smart-kid obnoxiousness), and his classmates responded with typical social behavior to pressure him to behave more the norm which then caused A to respond inappropriately that the school administration interpreted as potential violence. Fancy way of saying A liked to brag how smart he was, other kids subtly harassed him (Why do I keep avoiding calling it bullying?) and A responded so vigorously that he was the one viewed as the bully.
So we pulled him from the parochial school and put him in the local public school. I am happy to say he is thriving. His grades are A's with the occasional B thrown in. He did get into an altercation on the playground about 2 weeks before Christmas (there is a pattern here) that was quickly resolved by the principal and the school counselor. He also was involved in an incident with a neighbor boy but thanks to a persistent Mom, It did come out that A's story was the accurate one.
But overall, A had a lot of friends. They do seem to shift. He'll play with one kid for a few weeks and then find another. But there are plenty in the neighborhood. He is learning to distance himself from the neighbor who seems to cause him a lot of problems.
I am very happy with my decision.