I don't think there is a perfect solution so the one currently in place seems as good as any and certainly better than awarding 3 points to us as I doubt we would have scored if we'd played all weekend! we did nothing wrong but we didn't do anything to deserve picking up the full three points...
In both your example and Turkeys there would be an obvious intent to benefit and it's nothing like a rather stupid oversight on a loan player who had already been there for a month. I think the FA may do more than just deduct 3 points if any club were to be as stupid as you and Turkey are...