I had an idea for how to allow the player to satbomb quest important planets without any problems. One idea that sounded okay is to borrow from Morrowind and warn the player that "the threads of fate will be cut." The problem with this is the special treatment for quest related planets feels a little out of place... granted, it's not as out of place as the current immortality those colonies get, but still.
After looking at the luddic shrines scattered around the sector, I've been thinking that a better solution would be to give EVERY core world at least one quest chain it's a part of. Then instead of making all of them immune to being wiped out, you can just give the player a generic warning that reducing a planet to rubble will break ANY and ALL questlines associated with the planet that you haven't finished. You can now slap this warning on every planet because it's always true. Now if the player goes to satbomb somewhere like say, chicomoztoc, they can actually face consequences for their actions while being aware of what they're getting themselves into. For planets that are part of the main questline it's probably a good idea to retain immunity to de-civilizing from low stability, although maybe a toggle in the setting file for this would be good.
Now that I mention it, I think it's at least worth adding a toggle in the settings for the immunity, even if the rest of my idea isn't added. Casual players can have their guard rails in place and experienced players can go into the settings and take them off.