Good questions. I think they will need to still play out the scene. The question is how Emma and Regina end up getting back from the dream world now that they wasted the magic bean. Maybe the stabbing scene happens in the dream world? I have no idea why Gideon wants to kill Emma unless he is the villain to Emma’s savior now that Regina is no longer a villain? Maybe the Dark Fairy wants to maintain the balance between good and evil?
Some good points. Emma is definitely lacking a villain, especially now that EQ is caged up as a snake. I think your idea of trying to maintain a balance of good and evil is great. I also think (going back to the idea I had a few days ago) that maybe the sword will kill the darkness inside of Emma to help the balance of light and dark be restored (or to help her perform a huge task).
Keeper of Regina's bravery