This problem has been around from the beginning. The problem I have with it is that there is no way to stop it or even effectively manage it.
You don't have to take over independent colonies to make this a problem. The alien colony just have to be near by for their population to start showing up on your worlds. This is what I can not stand, the lack of a choice. I can choose to invade, use a colony ship of another alien race, or to take over an independent colony, but the passive infiltration of aliens race can not be stopped except by distance. Which sucks.
I do not have a problem with the penalties, because adding alien races to your empire has a lot of benefits. What this game needs is the ability to control and manage it. To manage it you should be able to sort by population type on the colony screen. It should show the ratio of comparative numbers of each. Ideally, you should be able to transfer aliens around your empire easily e.g. to make worlds entirely alien or dilute the theirs across your empire, etc. Rebellions shouldn't just happen either, you should have time to do something about it.
There should be new tech, which reduces the impact of have multiple alien races. The should also be new tech which reduces war weariness because there is point in this game where all that is left to do is to eliminate all of the other alien empires. Whichs is almost impossible to do now.
Their are also way to many Trekies and Star Wars fans on this forum. They need to keep their ideological bullcrap out this game because it isn't a Star Wars or Star Trek. That is what modds are for after all.
"Good, evil... I'm the guy with the World Destroyer"