There is a distinct sense of order regarding the school, the Vigils, and the chocolate sale. This order is created by history but it is perpetuated and enforced by those in power, those who are invested in maintaining a certain status. Those who "dare disturb the universe" pose a threat to the established authorities.
In Chapter 6 Leon hypocritically praises Bailey for being "true to himself." When Jerry exhibits just this quality, Leon does all that he can to break him down.
The order in the school that Jerry upsets in the novel is directly related to power. By refusing to sell chocolates, Jerry is initially going along with the Vigils and, in doing so, demonstrating the power of that "secret" group. By carrying out his assignment, Jerry is proving that the Vigils have power in the school.
This, of course, also proves that the school and Brother Leon do not possess absolute power. Brother Leon cannot force Jerry to sell the chocolates, despite his position of authority.
When Jerry disobeys the Vigils by continuing to refuse to sell chocolates, he proves that the Vigils also lack the power to determine the course of action of an individual.
At the novel's beginning, Archie and Brother Leon are the characters in positions of power. By the novel's end, Jerry also occupies a position of power. He has upset the order of the school by proving that an individual has power too, regardless of official authority (like Brother Leon) or group affiliations (like Archie).
Jerry's example is a potent one, despite the fact that he is defeated in the end. Before he is beaten up, Jerry shows the school that individuals have power too. Conformity is a choice, not a necessity. Jerry ultimately disproves Janza's choice bit of wisdom:
"The world was made up of two kinds of people—those who were victims and those who victimized."
Jerry proves that this equation does not describe everyone, at least not all the time. For a good part of the novel, Jerry is neither victim nor victimizer.
The theme "disturbing the universe" applies to The Chocolate War because Jerry Renault decided to question the entire system of the chocolates. Usually, every student sells a certain amount of chocolate boxes, no matter what. No one ever refused to sell them. Trinity is a school where privacy is nonexistent, where teachers intimidate students, and where students brutalize one another. Jerry took up an assignment from the Vigils to refuse to sell chocolates for 10 days, to mess with Brother Leon. However, Jerry decides to refuse the chocolates forever. After the 10 days, he keeps saying no, and this is messing with the sales. He refuses and accepts the consequences of his actions.
The way that the theme comes into play is that Jerry dared to question and "disturb" the perfect sales.