The question derives from TS Eliot's "The Love Song of J. Alfred Prufrock," which concerns a man growing old, wondering about his worth, nervous about what others think of him. The phrase in the poem can be understood as rather humorous, for all the speaker intends to do is ask a woman a question, and that surely would not "disturb the universe." The point is that often we think our actions are greater than they are, which makes us afraid to do anything at all, to take any risks in life. Using this direct quote from this famous poem is a literary device called "allusion," which asks us to read this part of the story in terms of the poem alluded to.
I think the statement is a challenge, asking whether a person will dare to be different, to "march to the beat of a different drummer", to quote loosely from Thoreau. It asks whether a person is willing to go against the flow, to NOT do what everyone else is doing just because it is expected, and to take the consequences of the choice.
In the context of the story, Jerry looks at his father's very ordinary life and asks, "is that all there is?' He doesn't want to just coast along and live a life of mediocrity like his dad, he wants to make his own decisions, to take charge of his own destiny, so to speak. When his assignment from the Vigils is over, the easy thing to do would be to just sell the chocolates like everyone else, but Jerry at this point is tired of doing things just because he is told to or because it is expected, so he "dares to disturb the universe" and continues to refuse to participate. Unfortunately, he finally concludes that the consequences of daring to be different are not worth it.