If Kuma, as well as Bonney, had been presented as much more minor characters, then I probably would have been inclined to say that they would get a happy ending by the end of Egghead. But the fact that Oda has pushed this much development with Kuma this hard, presenting him as a self-sacrificing character willing to do anything for the people he cares for and passed on the story of Nika to Bonney, I’m inclined to think otherwise.
Keep in mind, this is the same manga that had Ace get killed in front of Luffy after he went through hell to save him, and Toko laugh at Yasuie’s death after she ate a Smile fruit.
I also get the feeling that Oda tends to not really focus on death unless it’s meant to forward someone’s storyline or have the stakes feel more personal. So if Oda had the plan of having Saturn kill Kuma while trying to save Bonney, and then Bonney inherits Kuma’s will to liberate people like Nika did, then I think that would stay true to the feel of the manga and not be out of place.
So I suggest this not because I don’t want Bonney to have a happy ending, but to suggest how Kuma’s death may further Bonney’s story to a more developed level considering how much Egghead has focused on her up to this point.
I think that as long as Bonney is with people like Luffy, the new Nika, then I think a happy ending for Bonney would still be possible. Whatever happens, I’m sure Kuma would be happy too, knowing his daughter is with good company.