Yeah, I can totally see them not using their free will. I guess it's a bit like they don't use their feelings much. Not because they don't have, them, it just doesn't occur to them.

God isn't around to give the orders so someone has to be giving them.

This is a really good point. And not only do they come up with them, they are also apparently okay with implying that they're God's orders when giving them to the lower ranks.