Just I dunno, sell the pops on the market so other empires, that actually want diversity, can buy them. Even if you don't put them all in a meatgrinder or something equally horrific. Honestly I am amazed that the feature to get rid of pops isn't in the game yet. It is a workaround mind you, not a solution. Or evacuate if you have the tech (gives you a nice little money boost and a Core-Species colony ship). Now, once you have all the pops you don't want or need in one system, raze it. Ideally you have alot of space there for them so you don't have to do this more than once every 50+ turns.
Use the spaceport to 'cart' all the pops you don't want to a system you have barely just developed. Horatios, you feel my pain of having surplus, already spliced minor faction pops amirite? This is a workaround until the game lets us purge Pops we don't want.
