Instead of going down this depressing route, why not just end it on a happy note and have Emma and Hook leave together on the JR on their honeymoon going on adventures off screen.
Henry.
Emma would never abandon him forever like that. Sure, they could do the whole “we got a letter from your mom today! She sure does miss you” but six years of this show have largely been devoted to the Emma/Henry relationship. Now you could argue that the Henry/Emma relationship has felt more or less hollow for awhile now (an argument I would make as well) but in the minds of A and E, it’s not. They don’t see it that way. And with one of the bigger themes of the show being abandonment and breaking the cycle of it, having Emma run off with her new hubby with a new life and leaving the son she broke the original curse with behind would be…distasteful. For a variety of reasons.