It is more an inquisitor problem, they do too much damage, and are far too hard to kill off.

So in this way assassins are underpowered v them...or you could say inquisitors are overpowered.

Inquisitors are just a pain full stop. So you go on a crusade to keep the pope happy, and he whacks off your leader/general? What is the logic on that? Are you not helping out the pope to start with? The whole aspect of this is at best a pain, at worst highly unrealistic. Just how does some dude in a robe and book get let into kill off a top general..? Just because he doesnt go to church! Come on CA you can do better than this...its just a wild variable put in to make life harder...very unrealistic...and slightly absurd.