If Loki didn't die, then there's a chance that Mobius might still be alive. Does "pruned" really mean 'killed'? I'm thinking it's more of a displacement. The Timekeepers might still be around somewhere (think the Mandarin of Shang Chi and Ben Kingsley's Trevor from Iron Man 3). They are cosmic entities and pretty front and center where Kang the Conqueror is concerned (and so is Ravonna, btw), and Kang's confirmed for the third Ant-Man film. So the Time-keepers might be off somewhere else and not involved with the TVA who are running things the way they think it should be run, but not quite the way the Timekeepers originally intended. Think of the Supernatural storyline: God has left heaven and the angels are running the show in his place. That might be what Marvel's doing here with the Timekeepers. Or this might be how they introduce Kang: Kang killed the Timekeepers a while back and the TVA's just trying to compensate.