As I said, it did not make sense for at least Shaka to die. Because Egghead isn’t even nearly over. The most pressing plotline is still not revealed and for this, we need Vegapunk and especially Shaka in general back in action.
However, we do not know what this new version of Vegapunk exactly is. It looks either like thrown together spare parts from each Satellite, except York. Or it also could be only Edison, who is only taking the parts for himself. Because, what I think is odd, are the speaking bubbles of Pythagoras, Shaka and Atlas, which are the ones, we always see, whenever we have someone talking through telecommunication in some form. So, while Edison talks normal, as we can see, he is talking using his normal head, the others are either within him as part of the new Edison-Vegapunk-Satellite. Or the others are talking to a new Edison from afar using telecommunication and only notice him using different parts of them.
Also, now that the Steam-engine has made Punk-Records float up, the WG has a major problem.
If the Satellites can leave with Punk Records, which the WG wanted to be safe and sound within their hands, the mission of Kizaru would fail partly. Because Vegapunk’s brain is one of the three objectives, the WG wanted at all costs for themselves. The Satellites fleeing with it (even if no one knows about them being on that cloud) needs to at least be met with some form of countermeasure.
Saturn said it very good: “With York, Punk Records and the Power Station in hand … we have secured access to the eternal flame. That result would have been more than adequate… but we had one critical hiccup.“ This means that the WG’s gains were satisfactory, but not enough to cover for the fail of letting JoyBoy escape and having Vegapunk talking about the void century. Imu did show everyone, what he thought of the outcome of the situation with killingSaturn. If now one of the three things that WG gained were suddenly `clouded-away´, at least the ones, who can fly and are able to reach it, would certainly try doing so – Kizaru with his Light-fruit. Oda even highlighted the importance of Vegpunk’s brain being lifted with highlighting Yorks speaking bubble in bold letters as she exclaimed: “He’s taken Punk Records!!”
In hindsight of Saturn’s demise: One thing, that Oda really wanted to show us, was, that Kuma as well as Bonney were given the opportunity to still beat Saturn for his actions against their family. And the only opportunity to do so was during everyone’s flight. Because right after they left Egghead, they would have not been able to get their revenge, due to Imu punishing Saturn for his bad performance, killing him in the end.