Why do the preacher's words disturb Brent in Whirligig?

The preacher's words disturb Brent because they reference his current situation. Like Cain in the Bible, Brent is essentially living in exile.
In complying with Mrs. Zamora's wishes, Brent basically becomes a sort of wanderer, perhaps even a "fugitive" from the kind of justice he thinks he deserves. He feels he should have been sent to the juvenile detention center instead of receiving probation. Above all else, Brent believes he deserves to be punished. The text tells us that Brent's reaction to the preacher's words is grief; he recognizes the preacher's quotation from chapter 4, verse 12 of Genesis: "When thou tillest the ground, it shall not henceforth yield unto thee her strength; a fugitive and a vagabond shalt thou be in the earth."
The preacher's words remind Brent of his dismal situation, his culpability in Lea's death, and the loss of his innocence. Brent already feels like a fugitive from justice, and he definitely feels like a vagabond, someone who has no home. With one singular action, he knows he has wiped out the life of an innocent girl, and he must live with this knowledge for the rest of his life. To Brent, the preacher's words are disturbing because they reinforce his dismal situation and highlight his sense of living under divine condemnation.