What is Elizabeth's proof that John is a good man?

In Act Two, Elizabeth says, "I do not judge you.  The magistrate sits in your heart that judges you. I never thought you but a good man, John . . . —only somewhat bewildered."
They have just been arguing because John had not originally told Elizabeth that he had been alone with Abigail when Abigail confessed that the appearance of witchcraft was only "sport." He has just revealed that he was, in fact, alone with the girl with whom he'd once had an affair, and Elizabeth becomes upset because he was "not open with [her]" when they spoke before. John loses his temper now, insisting that Elizabeth only judges him rather than looking for the good in him. Her response indicates that she does think he's a good man, and it is actually he who doubts it. We can assume, then, that the years John and Elizabeth spent together have already convinced her of his goodness.
Further, it is, perhaps, his guilty conscience that makes her think of him as good, too. True, he did commit a sin, but his remorse for it could be seen as evidence that he is good, as a wholly sinful person would likely not feel such regret.