I’d be OK with Emma having killed Merlin, because assuming that masked Dark One was his love Nimue, and she obviously got killed at some point, at least they’ll be together in the afterlife now if Emma offed Merlin to cast the Curse, and I figure Merlin would be happier there, rather than hanging around in the land of the living all alone.
Once she loses the darkness, Emma can be the next Sorcerer.