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.
I’m guessing the Black Fairy brainwashed Gideon into thinking that Emma needed to be killed for the greater good. So whatever reason Gideon believes could turn out to be false.