In act 4 of the play, at the trial of the protagonist, John Proctor, Judge Danforth asks Reverend Hale if he has heard of rebellion in the town. Reverend Hale responds with,
There are orphans wandering from house to house; abandoned cattle bellow on the highroads, the stink of rotting crops hangs everywhere, and no man knows when the harlots' cry will end his life...and you wonder yet if rebellion's spoke?
These four signs of ruin can be taken literally and also metaphorically. Orphans literally are wandering from house to house because so many mothers have been accused of witchcraft and imprisoned. Metaphorically, the orphans represent the people of the town who have been abandoned by, or separated from, those who should be their leaders—the egocentric Reverend Parris, the cynical and opportunistic landowner Thomas Putnam, and the self-righteous, sanctimonious Judge Danforth. The same idea, of the flock having been abandoned by the shepherds, is emphasized with the image of the cattle loose upon the highroads, the pain and anguish of the cattle, and thus of the lost and leaderless people of the town who they represent, implied by the word "bellow." There is an echo here of a biblical passage:
How the beasts groan! The herds of cattle wander aimlessly Because there is no pasture for them; Even the flocks of sheep suffer. (Joel 1:18).
The third sign offered by Hale, "the stink of rotting crops," of course literally refers to the fact that the crops are not being tended to because so many people have been caught up in the hysteria and imprisoned. The crops represent the produce of what is sown, not only literally but metaphorically, and, metaphorically, the town has sown seeds of mendacity and immorality and is reaping more of the same. In other words, the "rotting crops" represent the moral degeneracy which by this stage of the play has overtaken the town. There is again a biblical allusion here, to a passage from Isaiah:
So their root will become like rot and their blossom blow away as dust; For they have rejected the law of the Lord. (5:24)
And finally we have the line "no man knows when the harlot's cry will end his life." This literally means that the men in the town are fearful of being falsely accused by the women who claim that they have been possessed and, like John Proctor, being executed for it. Metaphorically, this quotation can also be taken to imply that the lives of the people are at the mercy and the whim of the aforementioned moral degeneracy (here represented by the "harlot[s]") which has swept the town. There are several biblical allusions that might be applicable here, but perhaps the most fitting is "the land commits flagrant harlotry, forsaking the Lord" (Hosea 1:2).
The lines from Hale are, I think, deliberately biblical in their symbolism. The town has forsaken, as Miller might see it at least, the most important teachings of Christianity—to love one's neighbor; to not cast the first stone; to act with humility, kindness, and patience. They have forsaken Christ (and indeed, the protagonist, John Proctor, is a martyr very much in the image of Christ) and have so become lost.