Violent Revolution is exactly right. Keep good relations with the Pope!!!! Give him gifts, do what he says. Have lots of priests which become cardinals which one day means your cardinal becomes pope.

Also keep the heresy level low in your lands through the use of your priests and cardinals. If your heresy gets high in a province, expect an inquisitor to show up.

If you keep the Pope happy and keep heresy low in your provinces, you will rarely have problems with the inquisition.

It is another part of the game which needs to be and can be managed.