Are you sure that you have your facts straight? I've not read the book, but the Enslaver Plague, which wiped out the Old Ones, and forced the Star Gods (C'Tan) into hibernation, lest they starve and die, was what I'd always heard had caused them to go into their Dormancy, rather than the Emperor.
The Emperor is seen as the Omnissiah, by the AdMech, but should this Machine God, the Void Dragon, rise, it's theorised that everything with a Machine spirit can be controlled by the Dragon, and those of the AdMech who follow the Omnissiah (i.e. all) will follow him, causing greater devestation to the Imperium than the Heresy, as the full AdMech will go into revolt, the vast supplies they hoard will be lost, and It'll be down to the Man Portable Weapons, and finally Combat Knives, as fuel and similar resources, from the complex weapons, to the bare munitions necessities, will eventually run out.