You could call the minister what his congregants call him. If you don’t feel comfortable with that, it is perfectly correct etiquette to call a Protestant minister “Mister” (or “Ms.” if the minister is female). This, by the way, is basically what your Protestant friends are also doing: They could call a Catholic priest “Father” as an acknowledgment of what a priest is called by his congregation, but if they consider that a violation of their conscience then they call a priest “Mister.”