That's something a lot of people missunderstand about storytelling. Just like Poud coming back doesn't affect the story, Kuma coming back doesn't ruin anything.
The impact of a death scene doesn't come from death. Its comes from EMPATHY. The reason this flashback work so well is not because Kuma faces a lot of struggle, its because we EMPATHIZE with him in front of those struggle. Same thing here, the impact of the scene don't come from the "death" itself, it comes from the empathy we feel toward Vegapunk doing something he doesn't want to do.
THis empathy, just like in the case of Pound, will not disappear once Kuma comes back. That's why One Piece is so rereadable. Even after death come back, we still feel for the character that we empathize with during those moments.
It’s possible that Vegapunk is not sure if it will work or not. But even without that, at his place I would still be devastated to have to do such a thing and lose a friend.