One thing that she says she is unable to do is to judge him on his decision of whether to confess. She wants him to make that decision for himself, without pressure from her. He asks her a couple times, wanting to know what he should do, and if confessing would be that horrible. But she remains neutral, stating, "I cannot judge you, John, I cannot!" and "Do what you will. But let none be your judge."
The other thing that she is unable to do for him is give him forgiveness for his adultery. This might sound harsh, but all that she is implying is that she is not God, and it is only God's place to forgive. Also, she says that "it come to naught that I should forgive you, if you'll not forgive yourself." She knows that if he doesn't forgive himself first, then nothing else matters, because he'll always be beating himself up. Then she reassures him, saying that whatever he does do, "it is a good man does it." This in essence is a sort of forgiveness from her.
Lastly, she cannot save him from his decision to not confess. At the end, Hale is pleading with her to try to convince John to confess, but she states, "He have his goodness now. God forbid I take it from him." The last thing that she is going to do is take away a decision that finally brought John peace, redemption, ability to forgive himself, and vindication.