If there was just a way to delete it with a confirmation prompt or something I presume that would work fine. I for one am actually pretty enthusiastic about that solution. Its somewhat hacky but it would do the job.
If you delete the way point it should also delete any colony there as well... but not necessarily the Habitat as you can move that.
If you want to move Habitats you basically need to delete the colony and create it again in the new spot as you can't move the Habitat with the people inside.
That is one major concern: What happens to the people when you want to move a habitat somewhere else or abandon the site? Also, this temporary colony shouldn't allow ground forces or installations of any kind, including infrastructure.
I don't see the problem with this as it is only you the player that decide how the rules should apply.
As to moving the habitat there are two ways... either YOU decide that you can move the habitat with the people inside it. You simply delete the people on the colony with SM, move the habitat and add the people back.
Or... you build a new habitat and move the population with colony ships and then move the old habitat.
You will also still face the issue with factories and other structures... are they on the ground or in space... If in space the NPR will still treat it as ground and can invade it.
In my opinion you should just treat this way-point as if there IS a small asteroid there and it just happen to be there all the time OR you simply towed the asteroid there using all of your tugs or something.
This would purely be a role-play thing so that is who you should treat it. You do with what you will.
You already can use SM to place a rock anyplace anyway and then put a habitat there, this would just make that process easier.
If you are after a proper mechanic for building a full habitat in space with factories and all that is a different matter and would need to be handled very differently, for now I think we need to mainly treat it as if the habitat actually is orbiting some sort of body (in most cases).