I appreciate you can achieve the same result with the editor or mods.
I would like to request an in-game vanilla feature for it

I agree it would be nice to clear up remnants somehow!

TL;DR
Add a technology unlock that allows you to glass (clear all player owned entities) on a planet's surface

What?
This could either be a tool which "destroyed" all player entities, but leave the underlying geography undisturbed.
Or it could act like a new landing site on the planet, essentially ...