Why does Elizabeth refuse to influence John’s decision whether to confess?
She feels he must face his own conscience and make his own decision.
She cannot feel guilty if he refuses to confess.
She cannot feel guilty if he does confess.
She feels that he cannot blame anyone but himself if he does not confess.
It is because Elizabeth knows John must face his own conscience and make his own decision. At this point, the only thing John has left is the ability to make the moral decision and to uphold the integrity of his name, both in the eyes of God and the good people of Salem.
This play is about judgment. "Let he who is without sin cast the first stone" (John. 8.7). Only the individual can truly judge himself and only that individual can confess or speak the truth of his own actions and thoughts. Elizabeth knows this, certainly in light of the town's recent witch hunt. After all the false accusations and condemnations, Elizabeth recognizes that judgment can only rightfully come from God and the self. Only John can judge his own actions and only John can genuinely confess. That's why Elizabeth doesn't even want to influence him one way or another. She doesn't want to play any role in a decision which must be solely his, if that decision is to be genuine. In Act IV, responding to John's request for advice, she says, "It is not my soul, John, it is yours."