I hate inquisitors too.

In my experience it has not much to do with difficulty. I am playing a HRE campaign on H/H and parallely on M/H. I ignore the pope in both campaigns so my relations a not the best (0 to 3 crosses at best).

I had very few inquisitors in H/H. I had quite a lot of them from turn 40 on in M/H. They burned every of my familiy members except two. After I was excommunicated one time they disapeared (ca. turn 80).

Now (turn 130) they come again but in fewer numbers. I kill them whenever possible. It is one of the most beautiful moments when my assassins succeed (which is not so very often although I have +10+ assassins).