Removing the Pope
Removing the Pope and all that comes with, the whole shebang, appears to work like a charm in MTW2: just remove the papal states from descr_strat, and make sure there are no regions assigned to them in Descr regions.txt, and that's all. UI is totally clean, and played quite a few turns - not a sign anywhere. Gosh, you do get a lot of messages as only faction on the map - biggest, richest, etc etc.
Edit the Descr regions.txt file and remove any reference to papal_states. You need to change the file properties so it's not 'read only'.
Edit the descr_strat file and remove the papal_states from the list of factions at the start, then further down put a ; at the start of each line in the block of text that details the papal_states starting resources, characters etc. You know when your finished because you'll come to the Aztecs.
And it does get rid of Inquisitors. -bodkin