Arthur Miller does present a situation of opposition wherein some people are falsely righteous and quite wrong-minded and those in conflict with them are characterized by honesty and integrity, by and large.
By creating two clearly and morally opposed parties, Miller succeeds in creating a scenario where good and evil are set against each other.
The lines between good and evil are fairly well drawn in The Crucible. In the most simplistic sense, the good guys win in this play. It's true many of them die, but they die as righteous sinners before God. "Good" is represented by those who stand for a just cause, who tell the truth, who repent of their sins, and who do what is right in the face of adversity. People like Rebecca Nurse, Martha Corey, John Proctor, Rev. Hale, and Giles Corey are all flawed human beings who stood for the right things. "Evil" is represented by people who, among other things, lied, unjustly accused, or sought revenge. People like Rev. Parris, Abigail Williams, and the Putnams all selfishly sought to gain from others' failures and are the primary cause for the deaths which occur in this story. The Court, and particularly Judge Hathorn, is another matter all together. The Court was designed to recognize and protect good while it exposed evil. Instead, the Court was moved by other forces and was driven by pride to support evil. The simplistic terms of good and evil can be used here, because Miller does clearly delineate between the two in this play. The battle between them is clear, and good does win...at a cost.
The theme of good versus evil is conveyed in the fanatic obsession of puritanism and witchcraft being used as a way to get people to be tagged, labeled, and in trouble. When Abigail got fired from John Proctor's house after having an affair with him she was clearly determined to ruining his life and that of his wife. The ability to manipulate, coerce and blame others led to a massive craze of witch hunting in the town that even John Proctor recognized as a product of revenge. The anger caused by the fighting for land, the anger about the affair, the manipulative ways of the elders, and the fear of being accused all combined into a perfect storm of good versus evil.