In fact, it's sad that the author humiliates the Gorosei
Tbf, it understandable why at this point.
Vegapunk created what he believes is his ultimate weapons, the Serephim. He's also explained that hes getting dangerously close to knowing shit hes not supposed to and it seems like the WG know something about that. Plus, Akainu did mention that Vegapunk escaping is a detriment to the Marines/WG because he essentially invented all of their breakthrough tech (meaning he can help Luffy get around it when the time comes).
Here I think they made the logical decision at least.