How 'bout you just tell people not to do anything fantastically stupid, and you won't have any problems?
I don't see a situation in which you'd have, say, a freighter docked to a cargo pod docked to a fighter docked to another freighter docked to a capship and the Volition Bravos, anyway. Capships dock to fighters and other capships, but you wouldn't have huge branching chains of capships, anyway, you'd have only one on one (and maybe on one on one on one on one), because you'd have to go out of your way from modeling the ship on up to make it able to dock to two or three capships at once, and since it'd look as silly as it'd really be, nobody would do that anyway. And capships don't need more than a couple dock points anyway. Freighters only dock to their cargo.
Honestly, the only reason someone would try to make a long, awkward, branching chain of docked vessels, and then try to
move them, is if they were looking for trouble in the first place. You can make the SCP idiot-proof, but you can't account for the creativity of idiots, or the extent they'll go to to **** themselves over, and I don't recommend you try. I can guarantee that if the sort who stick paperclips in wall sockets got their hands on a copy of the current SCP, they'd find a way to make it crash.
You're overcomplicating this. If you want, you can include a stern warning in the readme to make branched docking chains at one's own risk, but seeing as it's an extremely unlikely use to ever come up, and at worst the program will just crash, not leap off their hard drive, kill their dog, and schtup their mother, I think it's fair to say it's okay if someone tries once and learns their lesson.
And that's my contribution for the year.
