For religions, I may be talked into making the exact "discount" for religions a value the region lord can choose. Within some limits (i.e. not 100% tax reduction, but maybe between 0% and 90% in 10% increments). But that's definitely on the "post-release enhancements" list.
Why not start at 0% tax, and raise it over or above the region tax level, independently of it? One tax rate per temple, of course. It would provide the tension option without worrying about the scenario Bedwyr presented.
Other idea: Set an extra % tax for followers of certain religions. This would fit very well with the medieval setting, taxing religious minorities.
