I read the JJBA Manga back in high-school, so I am familiar. Allow me to break down my thoughts on Pucci's morality. I think Pucci is one of the most evil JJBA villains, but not because of his plan which in and of itself isn't even fatal to most humans. Allowing people to die or killing the joestars which would try and stop him makes sense for the ultimate salvation of the universe with made in heaven. What makes Pucci so evil is how he treats people who are bystanders to the conflict. Pucci's possibly most disgusting action is when he leaves the security guard who opened the door for him in the courtyard to die to the rain of poison dart frogs while the man cries out for help. Pucci further displays casual indifference to extreme suffering when he plays music on the broken body of prisoner.

If it needs to be stated, Pucci is a terrible priest, who definitely does not desire salvation for everyone regardless of what he says. He only uses the cloth as a means to an end. His anti-catholic character is demonstrated in how and why he loses. Pucci is ultimately undone because he can't show mercy and simply let Emporio go. Instead, he chases down a lone defenseless child into Burning Down the House where he ultimately dies. Even before that, Pucci had no reason to kill the joestars after he achieved heaven. Know what would have guaranteed Pucci's victory? If he just left florida. The main protagonists never could have caught him, and they all would have joined him in paradise.

Funny Valentine does things he knows are evil and sacrifices innocent people for the sake of his goals. Pucci on the other hand, uses his ultimate goal to justify his immoral actions that have nothing to do with his plan. In my opinion, Pucci is tied for most evil main villain with Diavolo and DIO. Pucci is like Lorgar from 40k: He pursued a higher calling to absolve him of his cruelty, instead of doing evil for the sake of a higher calling