The central conflict of The Crucible is one of integrity, seen most clearly in the play's climactic final scene.
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.
From the outset of the play we see characters slipping away from their personal beliefs and succumbing to the pressure of the group and its views. The moral weakness of the characters who quickly go along with the group (Parris, Mary Warren) are contrasted to the strength of those who stand by their personal beliefs and personal views (Giles, Elizabeth, Proctor).
Parris is the weakest character in the play, changing his beliefs according to what serves him best in the moment, and in the end begging for Proctor to confess his crime so that he (Parris) won't be blamed and killed for his part in the trials. We might argue that Parris has no individual conscience.
Proctor nearly gives in and publically offers a false confession but stops short when he realizes that he cannot trade his integrity for his own life. His integrity, his individual conscience, is too important to give up.
This idea is at the heart of the play as honesty and integrity are pitted against the force of public opinion which, when driven by evil and selfish designs, becomes thoroughly corrupt.
Proctor is honest, above all, with himself. To confess is to align himself with what he believes to be evil. The prosecution is the real example of the devil. All who consort with them, then, become true witches.