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).
There is a general problem with habitats that removing one causes overpopulation and unrest on the (former) host colony the following production cycle.
My point is that a deep-space station, which is what this hack is meant to represent, should not be able to use ground facilites or be vulnerable to ground assaults. 'Just role-play it' is not sufficient because the NPRs need to be subject to the same rules.
If we actually follow the special "colony waypoint" method none of this really matters (with the exception of moving orbital habitats that would still be an issue):
1st - You can still allow the normal ground installations, there already is a soft cap based on the no. of workers the stations at that waypoint can house
2nd - Attacking such a colony with ships means that you attack the habitats like you normally would - a destroyed habitat kills all population housed inside and a % of installations at that waypoint
based on the proportion of civies that were housed in that habitat.
3rd - Boarding combat is now the new ground combat - Still need some special rules for this case. Boarding in habitats may or may not allow lighter vehicles to participate (up to Steve) and the
amount of ground units available to defend will depend on the crew and the amount of troops waiting in the troop transport bays on the station (if any). Also in the case of conquest the
attacker gets a copy of the waypoint (if they don't have the same colony waypoint at the same position already) with their newly conquered station and surviving population (also with the %
of installations corresponding to that station.
Of course this is a much fuller implementation as opposed to treating the waypoint as a pseudo-asteroid that doesn't actually exist. IMO for it to make sense deep space colonies would need special treatment.
As for the overpopulation problem isn't really and issue. Yes when you move out a habitat its going to result in overpopulation in the other habitats. So move people out. Or Steve could tie population to habitats making them move with the station. The former is how it would work if this was implemented today so its probably simpler.