So it seems the problems people have with the holy war implementation you developed are two fold:
1: It's not conducive to roleplaying because a crusader will have negative piety while a murdering thug who cares nothing about the Pope will have positive piety.
2: It screws up certain mechanics like dealing with the pope (a crusader can't call on the Pope for any of those diplomacy actions) and depresses the dynasty score for those who engage in holy wars.
However, as a mechanic to prevent excessive use of holy wars, your implementation is pretty good, so mechanically it's good at preventing what it aims at doing. Now I have a possible solution if the constraints of modding allow it which would retain the beneficial slowing of the use the CB while avoiding the pitfalls.
Establish an increasing check for piety for a ruler to use the holy war CB, but rather the deducting the 100 to 250 piety for a holy war, you simply increase the cost of the next holy war. Here's a practical example:
All numbers assume that the holy war is for an adjacent county.
Holy war 1: The game checks to see if the ruler has AT LEAST 100 piety. If he does then he can declare war using that CB. No piety is deducted when he declares war.
Holy war 2: The game checks to see if the ruler has AT LEAST 200 piety. If he does than he can declare war using that CB. No piety is deducted when he declares war.
Holy war 3: The game checks to see if the ruler has AT LEAST 300 piety, and so on
With this, if it can be implemented, you could retain the effective piety requirement for each additional holy war, while not adversely affecting dynasty score, or hurting other gameplay mechanics like interactions with the pope. From a roleplaying perspective you also don't end up with defenders of the faith with negative piety and rutheless atheists with positive piety. It's also easy to convey to the player and can be summed up with one sentence, "Each holy war requires that you have 100 more piety than you did for the last."
Would something like this be possible to implement?