Ah, yes. The Clone Empress.
That's one I actually think they set up pretty well. Okay, sure, she's back from the dead in a world where the only way people come back from the dead is via cloning. Occam's Razor, she's a clone.
... That's if anybody dares to publicly apply Occam's Razor.
We're talking about a very, very religious society, one that believes in miracles and basically looks on battleships as cathedrals and lasers as the light twinkling through stained glass windows. Combat against the heathen is a sacred act. This society, riven with internal strife and discord, ruled over by a functional usurper (a certain dead Sani, ah, Chamberlain, was it?), finds itself under siege by a terrifyingly well-armed and well-prepared enemy, one capable of posing an existential threat to the Empire. (That may not be the reality, but considering the havoc the Elders wreaked, you can see how panic would start to spread.)
At the climactic moment of the conflict, a vision of godly power: a battleship piloted by a long-dead Imperial Heir swoops onto the battlefield and crushes the foes of God and empire in a single, swift stroke.
"Well, that's awfully convenient," say the skeptics.
"Silence, blasphemer!" pant the immensely relieved faithful. "This is an angel from God, sent to our rescue! Didn't you notice she just saved our bacon?"
"Still mighty convenient," mutter the skeptics, but bite their tongues lest they find them cut off-- and, in any case, the idea that somebody might have set the Elders up for Jamyl to blow up comes off horribly conspiracy-theory-ish.
So, Occam's Razor applied with a heaping helping of faith and general gratitude at not being overrun by barbarians: it's a miracle! God has raised Jamyl Sarum, granting her flesh once more, and armed her with divine weapons! You don't get more "Godflesh" -ish than flesh literally given you by God.
At a certain point, that's the simpler answer.