The game was written, and has undergone extensive testing, to ensure that the Pope is unkillable through normal methods. Rewriting game code to allow it may have unexpected consequences.
If you just want to play a scenario where you conquer Rome, then on the turn when you want to capture the city, use the Diplomacy feature of the Worldbuilder to set the Pope at war with you.
Make sure that you have units on hand that can reach, attack and capture Rome in that same turn, otherwise during the interturn the game will restore Peace and teleport your units out of Papal territory.
As there are many scripted functions for the Pope, the game may behave a little oddly at times after you kill him. Past bug reports where the Pope was somehow destroyed still had him declaring Crusades and the like. Presumably he was doing this while hiding out in some remote mountain monastery, Fisher King style.
Also, I haven't tried this myself in a full game so I don't know for sure, but it is likely that if you become unstable, the Pope may respawn.