Simplest is the elimination of 'population' except as a fluff number.
Replace it with Development/Infrastructure.
That can be "built" into the colony ship in the normal sense.
We already have "Infrastructure". While it's not inconceivable that population could be rolled up with infrastructure, we'd loose some interesting possibilities if these two concepts weren't distinct.
* Smart Weapons that kill civilians without destroying infrastructure. A cool late-game weapon. It would be a huge advantage to be able to conquer a planet without needed to rebuild the infrastructure.
* Humane weapons that destroy infrastructure and buildings while leaving citizens alive. (this is less compelling than "smart weapons."
* Abandoned colonies: I.e. you have development, but no people-- a boost for starting your colony
* Slow Evacuations/Repatriations: Ideally you should be able to remove the citizenry of a planets to allow a new species to settle without loosing the development of a planet.