If he is Bae. Magic cost him so much. It doesn’t matter good magic or dark magic. Both of them cost him so much. I think too that when he saw the magical object, being or whatever in the box, it was really ripping his heart out again, but for me he his Bae and as Rumple said of Bae he was always the better man and so he choose to let Emma rescue the people, find her family and if he knew that it was his father, trying to clean his mess, because a part of him thinks he is guilty for the curse too and was sad that he was the reason why his father became what he is and his leaving, that caused the curse.
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Heros don't get their Happy Ending!