Yeah, I’m not sure what they would do with Emma. The problem is that Evil!Emma wasn’t part of “Emma” in the same sense that the EQ is simply part of Regina. Emma was infected with Darkness and it was removed from her, but it was never part of her over all damage/psyche. Regina’s EQ comes out as part of who Regina simply *is* because the EQ was born during moments of heartache, loneliness and despair. The closest they can come with Emma is pre-S1 and S1 Emma, when she was jaded and aloof. But that’s not evil the same way that the EQ is “evil.”
If the rest of the town/characters are somehow infected with Jekyll/Hyde’s potion, I suspect there will be some sort of handwave that makes Emma “immune” to it because “Savior!”