I'd dispute that Freedom priests have to reject orders. This is a choice on the part of the player on how to interpret the alignment.

The actual Freedom Temple guild slant clearly prioritises freedom through awareness of knowledge and ability to choose. It doesn't preclude choosing to believe the Barony is an excellent structure for doing things and thus choosing to be part of the command structure, even when you don't understand the commands. You might break from orders at certain critical junctures ("burn the necromantic spell book" is one interesting crunch point), but for the most part you'd perform as part of the patrol.