Wasn't Bonney's whole goal of becoming a pirate was to find her dad and sail the world with him? Why would they separate if he lives?
I do agree that Bonney becoming a Rev is a terrible idea after what happened with Ginny however.
That dream isn't possible right now.
If they escape, and Kuma regains his consciousness and memories, both Kuma and Bonney will be wanted for:
-Attacking a Gorosei, which is pretty much the worst crime in the world
-Bonney controlling the Pacifista
It's not like they can go vacationing right now, Kuma and Bonney's wanted posters will be all over the world. It's like when people say Vivi is just going to go back to Alabasta; like, no, she'd get arrested and sent to Imu within a week, the WG has agents everywhere.
If Kuma and Bonney survive Egghead and tried to sail the world and explore it together, they'd get captured very quickly.
They need to change the world before they can experience their dream, I believe.