I think that assasins should deal better with agents such as Merchants, Priests etc, but should have a tougher time than they do killing royalty, especially the Pope.

Just because a Priest is more pious doesn't mean he should be any harder to kill. Often a Cardinal with say, 8 Piety, can be extrememly difficult to assasinate. But as soon as he is promoted to being the Pope my assasins can have a 2/3 chance of killing him.

It should be far more dependant on target type rather than target ability.