Ah i think I figured it out. Bonney was cast out of slavery because her mother's disease, but if VP cures her, Saturn is threatening Kuma that she'll be recaptured again since she'd no longer be sick.
So he then negotiates to grant her freedom in the end. Bonney doesnt know she was born a CD slave, thats the big secret and what I assume Kuma sacrfices himself over at least.
What I still dont get is why Akainu acts like she ran away from the govt though, that part I still dont understand