Elizabeth has grown spiritually, I think, during her time in prison. Where once she was quick to judge Proctor and to withhold her forgiveness, now she is free to forgive Proctor and to admit that whatever the problems in her marriage to Proctor, she had some responsibility for that:
I have sins of my own to count. It needs a cold wife to prompt lechery."
She realizes it is not her who is judging her husband, now, he is judging himself. She sees him as good; it is him who does not see himself as good: because he wants to confess a lie and live; because he cheated on his wife. This is why, although she wants him to live, she understands when he recants his confession. He can't live with himself if he judges himself as evil. He needs his goodness more than he needs his life. The Elizabeth who spent time in prison is mature enough to understand this although she rues the necessity and hates the false court and accusations that brought this cruel circumstances: so she lets him go:
He have his goodness now. God Forbid I take that from him."