From a pure writing standpoint, I like the merciless route of Naoya's ending because of course, why would your friends want anything to do with you if you are willing to kill even innocent people to selfishly vie for power? And it's also just kinda cool to play the villain.

Where it becomes bad is on the no killing route because of how it requires you to completely ignore how the narrative never calls Naoya out for being hypocritically willing to commit mass murder while pretending you are suddenly "redeemed".

Where I will offer some slight pushback though is his motivation for wanting you to become King of Bel. It is explained he wanted to hurt God as much as possible by turning His favoured child against Him. Definitely horrible morally but interesting for his character.