Kuma seems to have a good enough relationship with Vegapunk. Vegapunk was able to grant him his final wish as a human being, which was to program Kuma to protect the Straw Hats ship until their return. It is very likely that Vegapunk highly respects Kuma's strength, as he modified Kuma to be the prototype Pacifista, and he let Kuma do things that go against the World Government, as well as granting him his last wish by including a mission into his programming that Kuma himself had requested.
It is even shown that the bible he holds is his trademark. If that is true why would he sacrifice his consciousness along with his humanity if he lived life cherishing something that very much so represented humanity, freedom and free will?
If he much admired the prospect of free will, going as far as wanting his last wish to protect the Straw Hats ship, why would he even agree to losing his humanity and getting modified to a fully-fledged Pacifista?
Is it ever mentioned or is it just some extremely personal relationship stuff shared between Vegapunk and Kuma?