John Proctor represents the moral center of The Crucible. His decisions are representative of the two major conflicts of the play.
First, Proctor is challenged to decide whether or not to stand up to the townspeople as they persist in the fraudulent witch trials. Second, he is challenged to achieve moral integrity by honestly admitting to his own faults, flaws and shortcomings.
Proctor understands that if he goes to the court to tell the truth about Abigail and her lies, he will be subject to the court's punishment and to death. To save his wife, Proctor faces this danger and makes the decision to risk his own life to save hers. This act is honorable and brave. In doing this, Proctor expresses a strength that allows him to stand up to the majority of his community.
In the end, Proctor also achieves moral integrity by admitting that he is flawed. He had an affair. He is a flawed person, yet because he can admit to his flaws he remains (or becomes) a good person. This admission is in contrast to Danforth's refusal to hear evidence that would suggest the innocence of those he has sentenced to death.
Danforth is unwilling to admit his flaws and so becomes representative of a significant moral failure. Proctor, oppositely, demonstrates personal strength and moral resolve by admitting his flaws and forgiving himself for them.
In Proctor's final recantation of his confession and his refusal to put his principles aside to save his life, we see the triumph of personal integrity in a world of moral uncertainty.