The best interpretation of what Elizabeth means by "his goodness" in this context is:
John Proctor did something noble by not naming others and refusing to confess in the end.
In this moment, Elizabeth is recognizing that John has regained his integrity and moral righteousness by choosing to stand by his principles rather than falsely confessing to save his life. She understands that this decision reflects his true character and strength, so she feels that taking that away from him by persuading him to confess would be wrong.