Inquisitors are a horrible, horrible feature of the game. In the mod I'm working on I made them a Papacy only and I also set them as invisible like spies/assassins. I removed the "Grand Inquisitors" altogether. The advantages are as follows:

1) Inquisitors are now almost like a natural disaster, instead of something that is targeted. They are very random and because you cannot see them you never know where they will strike next, this seems dangerous but...

2) You don't need to send assassins chasing around the map looking for him, instead your security forces will deal with this pesky foreigner when he crosses the border. Or if he does get through he won't last so long and will no doubt meet with an "unfortunate accident".

3) You can no longer exploit them.

4) They no longer raise zeal - this is now the job of cardinals whom function much like Imams.

I also removed border forts, so the counterspying is now down to the local spies and assassins. They gain valour from this whereas with a border fort in place they do not as the fort always gets the kill.