Out From Edom: Book I of the Irredente Chronicles

A far-future theocratic space hegemony tries to preserve what it believes to be 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.