But the nuns with guns are the Sisters of Battle, not the Sororitas as a whole. As far as I know, the rest of the Sororitas are like actual nuns, who go around building Scholas, spreading faith, etc. A cool plot for them, in my opinion, would be a Joan of Arc-ish story.
Some peasant girl from a feudal world gets visions and messages from the Emperor (or not...) and rises through the ranks and becomes a Canoness or something. Then, after a game's worth of misadventure and witch-burning, she stumbles upon the truth about the Emperor not being a god and all, and has to either:
Accept it out of loyalty to the Emperor, tearing down the Ecclesiarchy and shattering the faith of trillions of people (whose faith may or may not be empowering the emperor).
Deny it out of loyalty to the faithful, letting them sleep peacefully at night, maintaining some semblance of unity throughout millions of worlds. However, the Imperium stays the overzealous, intolerant cesspool it is.
The Imperium might have been previously united because the Emperor was alive, who was gigantic and golden and invincible. But that won't work now that their glorious leader is a skeleton hooked up to life-support.
So, 40kJean's choice is to serve either the real corpse, or a man-made god.
Unrelated, but I wanted to know: If the Imperium is so reliant on the Astronomican, which is on Terra 'cause the Emperor is there, how did they Warp travel when the Emperor was alive and well (thus moving around a lot)?