Waste colonies (Stellaris)

To begin with, I'm still new to this game and only played a few games. I'm currently playing for a wide empire on version 2.3.3.

Causes of the problem:

Spoiler: Recently in this game I started the first war against crazy robots destroying organic matter. I defeated them quite easily and took over all their systems. This is where this problem appeared. In order to unite the systems I had seized isolated from each other and pave trade routes, it was necessary to capture several systems with enemy colonies ... But these refrigerators founded so many colonies that in one system there could be 2-3 colonized planets ... Well I captured 3 systems I needed and got 7 new colonies ... And then also space orchids, which also fought with these refrigerators, lost control over 3 more colonies ... and then bam before the war I had 5 colonies, and after the war became 15. And I wanted to go through this game, founding only 7-8 colonies. And those colonies that I received do not give my empire any benefit, but on the contrary. They add debuffs for exceeding the admin. limit, these planets have low stability and since most of them are only 30% suitable for my race, it is costly to maintain these colonies.
Now, from the story to the question:

Is there a way to capture an enemy star system that has an enemy colony without capturing his colony?

I tried raider bombing, but as it turned out after it, there is still a settlement on the planet. If I fought a war with the aim of destroying the "main threat", then why can't I just send ground troops to the colony so that they completely cleanse its surface of these washing machines, but not populate this planet, and so that it does not receive the status of my colony, but for the system to be mine. Of course, I know that the planet can be "cleaned with rays of goodness" with the help of an ear, but now it's an early stage of the game and I won't be able to build one for at least the next 100 years. What should I do? Thanks in advance for your reply.