Eddy’s answer makes it sound like something about emma (her saviorhood?) Threatens Gideon’s world. He needs to kill her so something else doesn’t happen on other words. Maybe Emma can destroy the darker realms Rumple teased in 610.
It could be that. It could also be that she isn’t just any old Savior, she is a Savior that has been instrumental in turning quite a few villains into Heroes and this could also be a threat as she is increasing the strength of the “light” side. It could also be what I said before, which is that by eliminating the Saviors (as Jafar has been attempting to do, and the Black Fairy probably is as well) they are protecting their realm and also “snuffing out the light” that protects the other realms so that they are susceptible to takeover/consumption by the darker realms.
A threat like this would really require everyone, including Rumple, to work together to prevent all of the realms being obliterated. This is potentially end-game stuff.