[Alneyan]

You can abandon the colony to kill off the remaining popultion: if you ask to keep your facilities, you *will* retain the colony, but there won't be anyone (so it won't function).

I suppose you could also use a Planet Destroyer if you want to kill them all without doing any abandoning, or a Star Destroyer if you have the resources (a Black Hole Creator if you want to make sure nobody is going to use this system anytime soon).