I just double checked to make sure that you removed the factions from the catholic churches and you have. If you can still build them then I think you have become a victim of the virtual store. Please follow this tutorial from step 3 onward and then delete the medieval 2 total war folder in the virtual store if it exists.
But first let me ask the question that I should have asked in the beginning: are you modifying the main game or are using a mod set up? If you are using the main game then I recommend to install my mod set up and copy your edited files in there. It is designed to make modding easier by removing the known pitfalls, simply start it by using the provided desktop shortcut.