You've evidently never seen it from the Farronite Republic side of things... god forbid we create our own realm after Allison's "Theocracy" imploded when she left...
Forming Farronite as a republic was basically spitting in the face of the church. If they didn't want people in the church reacting badly to that, they should've formed as a theocracy. Now they should deal with the consequences, and expect angry reactions when they demand to benefit from privileges given to the theocracies. It doesn't help that they tried to lead their armies against faithful to usurp a city for a heathen, and again were seen to be consorting with multiple enemes of the church.
Ironic that when everyone wanted Farronite to be the newest theocracy, they went republican, and now that they're a republic, they yearn to be recognised as a theocracy. If they'd been a theocracy from the get go, they'd have everything they wanted- a cushy seat on the elder council, their fancy republican titles, and their voting system.