Steve,
What about placing a retooling requirement for factories, mines, etc either recovered or captured through conquest in order for your Imperial population to use them. I mean, not everyone has eight fingers, four feet and six eyes. The retooling could be accomplished by combat engineers, or factories transported to the planet. This way you don't move into a planet the day after you kill off all the enemy citizens and start building missiles and heavy armor units with your own citizenry. Of course this wouldn't be an issue if you conquered the enemy, but for those races bent on domination through annihilation, this would be a hurdle they would have to get over.
Adam.