Brother Jacques seems to have some authority over Leon at first. He almost seems like a good guy. After all, he turns off the lights on the athletic field at the end of the novel, breaking up the raffle. But, Leon trumps him, and Brother Jacques lets Archie and Obie go free.
It could be that Brother Jacques is afraid of Leon and Archie in the same way the kids are. They could ruin his life and his career with a well-placed rumor. Of course, this is no excuse for going against his personal vision of right and wrong.