A lot of people really don't know how the Decree Passive works, so it's nice to see posts like this that understand. The Sisters of Battle are both military and policing force within the Ecclesiarchy, while also being autonomous from it with their own seat in the Senatorum Imperialis. Their loyalty and faith is unshakable, and they're more driven to root out corruption and evil within the church than the priesthood. As for "no men under arms," this does not exclude priests from being carrying weapons or men of faith from taking up arms. What it excludes, specifically, is military organization of men within the Ecclesiarchy. A priest may carry a gun and join in the fighting. A group of men may become crusaders or even a militia of the faithful. But the Ecclesiarchy cannot take them on as an official fighting force, and the priesthood may not order them in any official sense. They can at most be bodyguards. The ordering of such militias falls under Astra Militarum jurisdiction, and the Ordo Hereticus monitors them and makes sure they disband once the war is finished and that the Ecclesiarchy isn't giving them support on the sly.