My idea as to how this *should* work, while being legible to the player :
A faith value, separate for state and all non-state religions.
Picking a state religion gives it +1 faith.
The current "religious disabling" option would give +1 state faith, -1 other faith.
Various civics and leader traits also would have an effect on this, for instance :
civics :
state church : +1 state faith
free church : +1 all faith
inquisitorial : +1 state faith, -1 other faith
antireligion : -1 faith, and -1 extra faith for state religion
leader traits : (probably only for the first levels ?)
pious : +1 state faith
spiritual : +1 all faith
zealous : +1 state faith, -1 other faith
anti-clerical : -1 faith, and -1 extra faith for state religion
Then various stuff gives bonuses and gets disabled depending on the faith for each religion :
at 0 faith buildings only give small "secular" bonuses (some culture and tourism I guess ?)
at 1 faith you start getting some interesting bonuses like happiness and the +1 yields per religious spread for shrines
at 2 faith more powerful bonuses like the free promotions get unlocked, &c.
at -1 faith religious buildings get disabled
at -2 faith you can build inquisitors and remove the religions that you have -2 (or more) faith with
(at -3 faith you can destroy holy cities ?)
Then the different faith values for each religion would proportionately affect diplomatic relations ?
(Fist draft, there might be some tweaks needed, for instance getting -2 for inquisitors might be a tad too hard ?)