In once sense, the real message has nothing to do with the play ... although, of course, it does. Miller produced two works in the early 50's, one original ("The Crucible") the other an adaptation of Ibsen's "An Enemy of the People." Both these stories speak of individuals who stand up to the pressure/power of the states. Each of these is clearly a statement about the "Red Scare" and the investigatons of Joseph McCarthy. Miller was a target of these, and he clearly selected these two plays to support the position(s) of the accused.
Joseph McCarthy's efforts have been praise and reviled, but some interesting new information has come forward after some files were released in Russia that show that he might have been as vilified as the people he was investigating. Perhaps either side could have been the doctor in "Enemy"?
The clear message is that innocent people are being put to death, identifying the true nature of the court, the real evil in Salem.
Proctor withdraws his confession and changes his mind about admitting to being a witch. He would rather die than live the shadowed, hollow existence he would have by confessing.
Proctor feels compelled to reclaim his integrity, because he has not lived up to his own moral code because of his affair with Abigail Williams.
His very identity is tied up with rescuing his name and withdrawing his confession. John Proctor feels that going ahead with the confesssion, which is a lie, is in fact aligning oneself with real evil.
He is also inspired by Rebecca Nurse's refusal to confess.
Rebecca Nurse is a very religious woman, she believes that evil has now taken over in Salem. A truly pious and kind woman, she knows that Salem has gone mad when she is accused of witchcraft.
Rebecca Nurse's death is similar to when a saint dies rather than renounce her faith. She refuses to give the court authority over her integrity. Her soul is at stake, her relationship with God is at stake.
Her willingness to die sends the message that she too will not sell her soul to save her life, she is accountable to a higher authority than the court, God.
Miller is suggesting that the people brought before the HUAC should stand firm. They should be willing to allow their reputations and careers be killed rather than selling out and providing names of other suggested Communists. John Proctor & Rebecca Nurse are showing that same courage, by facing death rather than allowing their honor to be tarnished with lies.