That's a good point. My thought, though, is that the boy could have been killed for being a Catholic --- as the priest says --- without the killers necessaily being religious bigots. They could have been irreligious bigots.
Do you really think the killers were religiously fervent youths who had a theological dispute with Catholicism? After all, one can be unchurched, an agnostic, or an atheist and be murderously anti-Catholic.
You make a good point. True Christians, whether Catholic or Protestant don't go around killing fellow believers who are from a different tradition. I'm reminded of the story of the man in that part of the world who was asked his religion and answered that he was an athiest. Then he was asked "Are you a Catholic or a Protestant athiest?".