She shows herself unable to judge John's final decision precisely because she has been locked up for three months, unable to see him, which has give her lots of time to reflect and think about her life and what had happened to their marriage. Having been so judgemental and critical in the past, Elizabeth now realises that she has no right to judge another man, even her husband, for such a massive decision, and she recognises the complexity of the decision that her husband must make and the varying factors and different "pulls" that are involved. Note what she says to John:
It is not my soul, John, it is yours. Only be sure of this, for I know it now: Whatever you will do, it is a good man does it. I have read my heart this three month, John. I have sins of my own to count.
Elizabeth therefore has reflected upon her own life and mistakes, which has made her much less ready to judge others. She has come to the conclusion though that her husband is an essentially "good" man and therefore will make the right decision.