I find it kinda amusing how many of your features I'd like to see in my western european kingdom.
I'm writing that because, well, maybe special non-land holding is exactly what you need?
Few days ago I was thinking about alternative holding system: every feudal country has 1-7 manors(which represent land) and no more than one of each special holdings(which represent any source of power, thats not land). In this system temple/bishopric is special holding that represents church's authority and influence - similar to family palace from The Republic. Every bishop is de facto vassal and advisor of his count, but he has some targetted decisions he can use for or against his liege (for example tell his co-vassals that they should give count what belongs to count, or they'll burn in hell). If you are king, you have your own archbishop and episcopal conference, which work more or less that same. And of course you can give your land to church (manors(vanilla castles, cities and temples), counties, duchies...).The main idea is in fac introduction of Islamic clergy into the game, because it played (and still plays) very important role in the in Muslim societies.
In Ck2 the temple holdings are controlled by feudal holders, which is correct, because in reality the muslim clergy, unlike the Christian, did not control land. But with this step the clergy virtually disappeared, which is problematic.
The plan is to introduce an Islamic cleric - Imam - to every county (or perhaps even holding), a character which would be independent of provincial holder's will (would be auto-generated and not appointed by the player/AI). This Imam, or in larger realms collective of Imams, would represent a natural religious opposition to the player.
I'm writing that because, well, maybe special non-land holding is exactly what you need?