The VIZ translation made me understand the timeline much better. So: at some point, before Kuma is fully turned into a machine, Bonney escapes the government's watch and forms a pirate crew. Presumably to search for her dad, or just because she turned 10 and it was time to see the world. This is how she ends up in Sabaody and why she is a supernova - they gave her a high bounty with the hope of catching her swiftly!
This explains Akainu's comment: "When I heard that you had fled the government, a chill went down my spine". They had lost their leverage against Kuma before the operation was fully completed! Then Bonney is free again since Kuma fully became a cyborg. A bit weird that they let her go even though the newly-cyborg Kuma was just guarding the Sunny - I guess they either trusted Vegapunk, or Kuma trying to kill Ivankov was deemed enough.