The only answer to the inquisitors problem is the assassin. Inquisitors will always come. They appear from nowhere, in case there is a heresy in a province. The problem is that even when the heretic is dead, the inquisitor keeps on going to the another provinces. And since the AI hates you he keeps going for your people. In doesn't really matter haw much the pope likes you, ore what country are you playing. So kill them as soon as you see them, before they burnt to many man and get to strong. So if like to play on hard or very hard you don't have much of a choice, but to develop the assassin guild. One HQ is enough.