The poster in Jerry's locker reads "Do I dare disturb the universe?". So what does that mean? The word "universe" could be taken in several different senses, but first consider what it could mean to Jerry, and what it might mean to the readers of The Chocolate War.
While Jerry doesn't consciously understand it, at first, he is "disturbing (his) universe" when he stops doing what is expected of him. Specifically, he disturbs the universe of Trinity, which functions on a kind of social contract between the bullying Vigils and the weak and venal authority of Brother Leon. If that balance is kept, then things continue on much as usual. In the most general sense, this universe is upset by Jerry by his action of not selling the chocolates; he tips the balance of power away from the Vigils and Brother Leon, slightly, onto himself. They cannot compel him, no matter how he is threatened and even punished, to do as they say. Some of their power has been leached away by Jerry's actions. This leads them to do things that they would not normally do (such as the Vigils taking the extreme step of the boxing match to punish Jerry, and Brother Leon allowing this to take place). They are, in a sense, controlled by Jerry. An upset to the universe, indeed.
But "universe" can also mean something else. Jerry's private universe is profoundly changed by his actions. He knows his actions to be just, and therefore his character is greatly strengthened by it. He learns to endure suffering and isolation (even Goober deserts him) for a just cause at a young age. These are very important lessons which would not be learned by him, at this young age, if he hadn't stuck to his guns. His internal universe becomes other-focused -- he places more value on the justice of an action than on the convenience or easiness of an action. This is perhaps even more important than the change he makes to the Trinity "universe".
Also, a case can be made that Jerry's family universe changes. It has already altered irreparably with the death of his mother. Jerry, however, learns during this time not to depend on his father, who is in such a state of grief that he would probably not be very useful to his son. What happens when Mr. Renault learns about Jerry's defiance will probably change the nature of their relationship forever.
There are many meanings to "dare I disturb the universe?", but applying the principle in one's life could be simply not doing what is expected of oneself. To do this in the cause of justice and right would be the most profitable and best way to cause character growth, but it need not be as destructive and dangerous as Jerry's actions. Simply changing one's bad habits, or perhaps working proactively on relationships could "disturb one's universe" in a positive way.