Elizabeth asks John to consider his conscience. She tells him that many people have confessed and been let go.
When John Proctor is sentenced to be hanged in Act 4, Reverend Hale asks Elizabeth: “Will you plead with him?” (act 4). He wants her to use her influence as his wife to convince him to change his testimony. If John confesses, they will not hang him. Elizabeth and John’s relationship has suffered since his affair.
John asks Elizabeth if he should confess, but Elizabeth does not give him the answer he wants.
As you will, I would have it. I want you living, John. That's sure. Do what you will. But let none be your judge. There be no higher judge under Heaven that Proctor is! Forgive me, forgive me, John-- I never knew such goodness in the world! (Act 4)
She reminds him that he has to answer to his conscience. She wants him alive, but she does not want him to swear under oath to something that is not true. John does choose to testify, but he regrets it almost immediately. He knows that his testimony will be a lie, and therefore a sin, and it will rest on his conscience.