I see this as them calling Cavill's bluff. "If you won't come back, we'll just replace Superman with Supergirl". Thus still leaving the door open for him to come back. This could be an Earth 11 situation where she's from an Earth with reverse genders if we're talking about the multiverse. If this is Flashpoint, it could a situation where Kara came to Earth instead of Kal. Though how him going back and saving his mother would cause events to happen differently on another planet is anyone's guess. There's a number of potential explanations here.