What does Elizabeth mean when she says to John, "the magistrate which sits on your heart judges you"?
Arthur Miller’s “Crucible” should be read in the context of Protestant Christianity, in which the Church on earth is understood as flawed and sinful. In the sinful human Church of Salem, local politics and human fallibility (adultery, greed, bearing false witness) distort the justice of human magistrates. But as well as fallible human judges, there exists a true infallible judge, Jesus, who in Augustinian theology appears as the teacher, who renders true judgements not corrupted by human veniality. It is this inner magistrate in John’s heart to whom Elizabeth refers.
This quote occurs in Act II, while John and Elizabeth Proctor are revisiting the matter of John's infidelity with Abigail Williams. Earlier in the play, John was alone with Abigail for a brief moment, which rouses Elizabeth's preexisting suspicions. This leads John and Elizabeth into a thorough focus on what has happened before, and John grows upset with Elizabeth, saying, "I"ll plead my honesty no more, Elizabeth." Elizabeth attempts to reason with him, at which time he claims that he is upset with himself for confessing his infidelity in the first place, telling her she isn't God, and also saying, "Let you look sometimes for the goodness in me, and judge me not." At this moment Elizabeth responds with the line in question, saying, "I do not judge you. The magistrate sits in your heart that judges you. I never thought you but a good man, John - [with a smile] - only somewhat bewildered."
By this Elizabeth means that she is not judging John for his actions. She recognizes the act as a moment of bewilderment, and believes him to still love her. The quote regarding the magistrate means that the judgement of John is not coming from any outside force. Rather, John is the one judging himself. It is his heart that is the hardest on him. It is his conscience that is making it so difficult for him to move forward.