I'm also not 100% sure if the Asym can 'use up' all the available civilians or if ALiVE will just keep spawning civs and turning them to the dark side ;)
They won't run out, they are kept for the immersionz. They will however run out in the sense that it won't just endlessly recruit civilians as long as the HQ is active, it will eventually cease operations as to prevent too much spam.