Think back to uni in their promotion season from div 1 and they had all their points taken from them for a misregistration of a player. Why is this any different? There is a precedent of this so it sticks.
Happy with the points being taken off them, don't see why they are awarded to the opposition with a 3-0 score line.
This it the standard ruling NZ wide, if not world wide.
Since the MPL commenced in 2002 their have been seven incidents of rulings of an ineligible player with all seven resulting in the 3 points 'awarded' to the non offending side.
Also two cases in the qualifying league has cost two teams promotion for playing an ineligible player(s).