Maybe I am feeling cranky, but this looks like a move on somebody's part to get this child on the "church" team. We lived near a mega-church once, and maybe it was just them, but they were totally insular, had their own elementary school, which only some of the children attended as it as expensive, tried to get their own teams in park department leagues, which can be fine if the league allows groups to enter as teams, and the kids (from the neighborhood) acted like my kids had horns and tails because we not only did not attend mega-church but -- gasp -- were not only not Christian but actively Buddhist. The ones in the public school, we heard from other sources, were very cliquey and self-righteous. This was but one of the reasons our children attended deliberately inclusive (and also expensive) private schools, with their own leagues, and private, deliberately and actively open to all, camps.
Our kids had (and have) tons of non-Buddhist friends. It teaches the First Amendment, open-mindedness, respect for others, and strengthens one's own faith. We encouraged this. Tolerance is a Buddhist virtue.
I am not mad at Christians, atheists, FSMs, or anybody else. I do not ascribe these difficulties to all mega-churches or mini-churches of any belief system, or all people in this one. This was our experience with one such nominally Christian body, and the insularity and what OP said about the church trying to keep their children together that leads me to raise this possibility. OP was right to keep her child where he is comfortable given the circumstances. Director's comment was ignorant at best, and shows he was not listening, which is ride.