A few things regarding Bonney, Kuma and Vegapunk:
We know that Kuma agreed to be transformed into a weapon that the WG can use. We also know that Vegapunk did the modifications and knew that Kuma had agreed to be transformed.
Then thereafter came a time, when Bonney was held hostage by the WG and had to escape and formed a pirate crew. It was Akainu, who again found her and took her in as a captive in chapter 595. By doing so, he even let it slip that he was afraid, as he heard that Bonney had escaped. And by saying that, the fleet admiral hinted at a still hidden aspect of the agreement Kuma made with Vegapunk.
Because, with this chapter, Kuma only agreed with Vegapunk to donate his blood for the Pacifista-project. There was no talk about Kuma being turned into a cyborg – not a single one of it.
With the deal between Vegapunk and Kuma set in stone, there must have been an influence to rearrange the conditions of said contract. And the only influence that so far has been revealed, is Saturn. So, it is very likely that Saturn has put his foot down and forced Kuma to accept being turned into a mindless weapon/cyborg completely.
And this narrative would also fit perfectly into the picture of Bonney wanting to kill Vegapunk:
Young Bonney was on Egghead with her father – a WG-island. She thinks that the only person, who knows of Kuma being on the island, is Vegapunk himself and no one else. If someone was now to take her into custody of the WG. And in addition to that, if she was to find her father being turned into a living mindless weapon, Bonney would put one and one together and think it was Vegapunk, who made the call to the WG and turned her father the way he now is.
For Saturn the only problem would be making Kuma do what the Gorosei wants. And this chapter gives us a hint what he uses to build pressure. Here Kuma tells us that “Honestly…if it’d cure Bonney, I would’ve made a deal with the devil himself.”. And this is very important, because Oda has even highlighted this sentence bold. Saturn somehow being able to threaten Bonney would make Kuma agree to his terms. But Saturn would have also need to make Vegapunk agree to those terms, because he is the only one, who could modify Kuma in the end, even if he did not like it, like he tells Bonney in chapter 1072 in a roundabout way.
Bonney being threatened by the WG and serving as a bargaining chip in this deal would also explain, why Vegapunk refused to tell Bonney why her father didn’t want her to know that it was because of her, he made the deal to turn himself into a mindless weapon. It would have hurt her – and it did, since she did cry the whole night, like Luffy mentioned in chapter 1090.