Emma’s magical potential is huge, but dark magic we’ve been told corrupts you, for once it tastes you, it wants more. This could seriously be a huge potential problem ahead for Emma, and she may need someone like Neal to help her stick to the path of light, rather than following in the dark footsteps of those who were seduced by power.
Neal has seen first hand how dark magic can corrupt. I do think there was a flash of concern on his face when he discovered that Regina had been teaching Emma magic. Even if he’s not fully aware that his father is the one who taught Regina, who is now in turn teaching Emma, he at the very least knows what kind of magic Regina practices.
Given that Emma is TL magic incarnate, I dunno that she could even be able to fully embrace dark magic, but having seen his father fall to dark magic, I can’t imagine Neal just sitting idly by and watching without being worried about it if Emma continues to take magical instruction from someone who only knows how to do the dark stuff. Maybe his concern over it, and reaction to it, if he tries to convince her to stick to the light side, will ultimately be what proves his love to her and makes her believe that she IS worth fighting for, and that they ARE worth another chance together.