There’s so much we do not know about why he thought he had to leave, but we know he thought that. He’s said so and the writers have said so.
What we do know is terrible things would have happened if he stayed, and that the curse could also be broken on Emma’s death. So the simplest thing for me to think there is that Pan would have killed Emma. Why not? Pan needed Henry’s heart and apparently could use it from birth (or planned to have the Darling Bros raise him). Now if Emma were not with Neal, then perhaps Pan could not track her to kill her. He might have been able to track Neal due to Blood Magic. So Neal had to stay away until after the curse.
Now I don’t KNOW for sure, but it would be a possible story that the writers have yet to reveal, but as I said, people come up with all kinds of things they don’t know either about how Neal could have stayed and that’s again, speculation.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass