Change the civie colonization logic so that they can create their own colonies and start populating them wherever there's a habitable planet (e.g. colony cost less than some threshold like 2 or 4 or 10). In other words, allow civie colonization target worlds to pop up like civie mining complexes do.
It just occurred to me while answering a question about the source/destination that a nice realism effect would be for those pesky civilians to go where they want to, rather than where you tell them to. This would probably have an interesting effect on the diplomatic game - your civies would be sneaking into alien empires and setting up colonies. Further mechanics along this line would allow players to "disavow" a settlement in alien territory (so the aliens wouldn't want to go to war with you). If the aliens attacked others of your species though (even if they were disavowed) it would generate negative diplo points in your population towards the aliens. This would lead to the need for a civ to police its own border to keep its civies from entering alien space; "arresting" a civie ship would presumably lead to warning points (the ones that happen when ships are blown up to tell the civies to stay out of a system) for its destination in alien space so a civ wouldn't have a never-ending stream of civies trying to cross the border. And so on....
If one were to do this (especially for 10) it would probably be best to put a "happiness" score on each population, which would be some combination of unemployment, wealth generation, %consumer goods requirements satisfied, colonization cost, total population, etc. (I really like the consumer goods one.) The flow of colonists could then be driven by a desire to go from unhappy planets to happy planets. The trick would be to set it up so that people would want to emigrate from high population worlds like Earth to low pop/undesireable worlds - you'd probably have to throw in a factor like log(total population+1) to the unhappiness to represent the "new frontiers" desire of a few people to move from the "city" to the "wilderness".
John