Out From Edom: Book I of the Irredente Chronicles

A far-future theocratic space hegemony tries to preserve the human genome by limiting technology. When an unknown enemy begins wiping out hegemony worlds, the complacent, ineffective government is weakened. A genetically-errant urchin and a reactionary priest set out on separate voyages, each discovering shocking truths about the nature of the threat to the hegemony.