It’d get messy from the moment Emma came back and became part of the equation. If there’s this guy that Henry has already gotten to know a bit, and then suddenly he discovers he’s his father, so they want to get to know each other more, but Emma tries to keep them apart, that’s ripe for angst on all sides.
If Henry’s father comes to town, and Emma instantly wants nothing to do with him, and doesn’t want Henry to know him, that’s exactly the situation there was in season 1 where Emma came to town and Regina tried to keep her and Henry apart. So unless they just wanna re-hash the same storyline, they’ve gotta put a different spin on it somehow. Having Henry and his father establish a friendship before having any idea that they’re father and son, and then having them torn apart, would put a different spin on how it happened in season 1.