There should be an option to evict specific populations from planets, however this shouldn't come without a trade off. This is an alternative to the popular idea of being able to purge unwanted populations (which we also need, and should come with happiness/influence costs).

My idea is that an evicted population would make its way (either by ship or behind the scenes) to the nearest faction which currently allows the pop (following this thinking, there should be an option to choose which pops are allowed in a faction), giving that faction a free pop. Evicted populations would prefer their native faction when deciding this, and if there is no available faction, they will join the nearest pirate faction, increasing the strength of the next pirate fleet.

Evicting should come at a production cost as well to cover the practical issue of rounding up and providing transport.

Edit: I think there could also be a diplomatic penalty with whichever population you are evictings native faction, but it would be less of a hit than if you straight up purged a population.