Good question, it might be possible, but it still takes time to fully control a person stronger than himself. It took him a while to control Vegeta, but if it's a god of destruction like Beerus then I think he can't do it since Beerus is on a different league than Goku and Vegeta. With God ki, all the power is built up inside rather than letting it out like super Saiyan and past that. So I don't think super baby will be strong enough to stay inside Beerus to control him. Super Goku and Vegeta obtained God ki, so if they go to ssj God or ssj blue then super baby wouldn't be able to control them.
Then I got an idea just become vegeta pretend as him then get the dragon balls and go back in time then. Wait for lord beerus then blah blah blah then train there get god Kai then take control of him, ez
