At first, John Proctor's dilemma is how to handle Abigail Williams. Although he's broken off their relationship, he knows what Abigail is like; he knows that she might gain revenge for his dumping her. At the same time, John still retains feelings for Abigail but is determined to do the right thing and renew his commitment to Elizabeth.
Later on in the play, John is faced with an even more difficult dilemma, a seemingly insoluble moral quandary. When Abigail starts making false accusations of witchcraft against Elizabeth, John knows that he must reveal his adultery in order to save his wife from the gallows; he must expose Abigail as being motivated by revenge after John ended their illicit relationship. But doing so will lead to John's good name and reputation being tarnished in the eyes of the people of Salem, and for John that's a very serious matter indeed. And when he himself becomes the subject of false accusations, he is faced with yet another dilemma: whether to save himself or the good reputation of the Proctor name.