Decree Passive
So after the Age of Apostasy, the Imperium issued the Decree Passive, that said the Ecclesiarchy could no longer have "men under arms" to prevent them from taking over the Imperium again.
In strange amount of rules lawyering, Thor said that the Sisters of Battle should be exempt, since they were women under arms. Everyone agreed to this for some reason.
On top of that, the Ecclesiarchy has other ways to get around the Decree:
- Crusaders
- Frateris Militia
- Shrine world PDFs
- Any random mob of pitch-fork and torch bearing citizens a local priest can drum up
- Cult of the Redemption
In short, the Decree is just an excuse for the Church to have an order of sexy battle nuns.