That’s EXACTLY what I think will end up happening. Not this seaason, but season 2 is definitely a possibility. I’ve actually read theories that said Mr. Gold wants Emma to become the new Dark One. However, those theories were created before we found out about Mr. Gold’s mission to find Baelfire and the lack of magic in Storybrooke.
I could definitely see Emma trying to control the Dark One. The only thing that worries me about it is that Emma could end up being fooled like Rumpel was. I don’t think Emma would ever kill Mr. Gold, but I do think that he could end up manipulating her into thinking that she has the power while the real power secrets still lies with him. SCARY!!! 😯
Another interesting aspect of this the cusody battle is the father. It all depends on how it turns out. If Mr. Gold gets custody of Henry due to DNA evidence (Baelfire theory ) then Emma won’t be able use the law on her side. The law will clearly side with Mr. Gold. So, she may end up resorting to drastic means.