The rule is a FIFA one that The FA have to apply. It is to stop players serving bans or already registered overseas signingfor other clubs. (Pease correct me if i'm wrong in this.)
The rule should be amended so that if it turns out that the player was not under a ban and not still registered, the punishment is merely a fine for not handling the paperwork properly. To punish a club with a points deduction when there was really nothing to stop the player playing for his new club (a la Robinson) is just madness.
As an aside, if Wimbledon took this player straight from a Welsh club then they were a bit naiive. As came out in the Robinson affair, GH was fully aware that players moving between, say, Altrincham and Colwyn Bay would need an ITC, just not Accy to Alty.