Elizabeth utters this phrase at the very end of The Crucible, and it is very significant because it is the reason that she gives for not stepping in and pleading for John to not confess in order to save his life. She is standing there, watching her own husband go to the gallows to hang, and doesn't beg for him to reconsider; instead, she says that he finally "has his goodness," and that she wouldn't dare interfere with that.
What Elizabeth means is that for the first time in a long time, John actually felt like he was a worthy, righteous, brave man. He had spent the last long while feeling guilty over his affair, feeling bitter and upset at himself, feeling unworthy to be in the presence of more pious people, and feeling conflicted about his faith, minister, marriage and goodness. He didn't like himself very much. In fact, in his conversation with Elizabeth before this moment in the play, he confesses how he "cannot mount the gibbet like a saint...I am no good man." He has no confidence in himself; he feels that if he stands all self-righteously up at the noose, touting his honesty before the world, that it would be a hypocrisy because he is not a good person. He has lied, he has committed great sins, and to go to the noose pretending that honesty is part of who he is, then he is fooling no one. He feels intimidated at the prospect of going up there with the likes of Rebecca Nurse, renowned for her piety.
However, by the end of the act, John has made up with his wife, been forgiven by her for the adultery, and stood his ground on the issue of not confessing to a crime he didn't commit. He refuses to confess and have his boys see his name on a list of "witches." He refuses to leave them the legacy of a weak liar. And the very act of standing his ground and deciding not to confess at the cost of his life is what, in the end, convinces him that he does have some goodness in him. As he tears the confession he states, "I do think I see a shred of goodness in John Proctor," and for the first time, is at peace with his life, his sins, and his past. He is at peace. That is what Elizabeth means--he is finally at peace with himself. If she intervenes and forces him to confess, he won't have that anymore. She respects his self-dignity more than her own selfish desires for him to live. I hope that helped clear it up a bit; good luck!