Kuja: You two just don't get it!
I need an eidolon more powerful than Alexander! An eidolon with the power to bury Garland! His powers are so incredible; I cannot even come close. I must destroy him before Terra's plan is activated, or my soul will no longer be my own!
When the true people of Terra awaken with the assimilation of Gaia by Terra, Kuja will have served his use and the soul he was given would probably go back to whomever it originally belonged to.
His attempts to conquer Gaia and Terra serve not only to prove what he believes, that he is the strongest being in existence, but also to save himself.
His final decision to kill everything when he finds out he will die has nothing to do with being spoiled. Regardless of his treatment or what he was born, Kuja had a very large ego. He had spent his entire life denying who he was and trying to achieve the power he felt he deserved. And he finally had it...only to have it rendered meaningless in a few minutes. His conclusion then was "well I'm the best thing alive. Why should the lesser beings be allowed to live if I can't?' which makes perfect sense if you factor in his narcissism.
Kuja's final actions were very human. To save himself, he decided to destroy the origin of life. His very existence, and that of everyone else, will be nullified as if they had never been. He won't die that way. At least not in the conventional sense.
Also Garland was neither good or evil and certainly not cruel. He was also created to serve a purpose just like the Genomes he made. All he could do was resurrect Terra...that was his purpose.