1. You need to build your forces and bide your time, taking rebel settlements and waiting for your enemies to make a mistake with the Pope. And if that sounds dull, it isn't, because they make alot.THEN you can strike, fully justified and with no fear of repurcussions.
Understanding how to do this directly negates the problems you mention in points 2 and 3.

I had a crusade leading general with 0 piety and some kind of negative piety witch in his retinue, but as I had followed the plan outlined above, he passed 7 or 8 inquisitors on his journey and wasn't bothered once.