There are a number of possible answers to this question, but I think that the two most believable ones are "spite" and "revenge". Brother Leon, the assistant headmaster only filling in while the real headmaster is ill, is not as good a leader as he should be. He is eager for power and is attempting to make a name for himself by the huge success of the chocolate sale. Not content to let things go on normally, he enlists the help of the Vigils to ensure that the chocolates are all sold. This happens not because of Brother Leon's great skills as a headmaster, but through the force and coercion of the bullies of the Vigils. Brother Leon makes a deal with the worst element in his school, in order to further his own ends.
Jerry is the only boy (besides Goober, who eventually gave in) who stands up to the Vigils and doesn't allow them to bully him into the chocolate sale. His defiance becomes for him more than just a refusal of a trifling school fund-raiser: it becomes a matter of principle. Jerry refuses to sell the chocolates because he will not be bullied by the Vigils. He knows he will eventually fail, and may have horrible consequences befall him, but he stands up right to the end anyway. This non-conformism and strength of character is unprecedented at Trinity, and also inspires other boys to stand up to the Vigils and to the venality of Brother Leon. Brother Leon sees Jerry for what he is -- a threat to Leon's (and the Vigils') authority) so he allows the horrible beating of Jerry to take place. This kind of corruption of authority, through selfish desires and collusion with an essentially gang-like secret society, forms one of the main themes of the novel. Leon, a man of the church and entrusted with the minds and souls of a group of young boys, commits a truly horrible betrayal when he allows the Vigils to rule his school and, eventually, to punish Jerry so severely.