That's obviously because the individual teams device their race strategy including fuel loads, tyres and pit stops etc around an expected race distance which was not anywhere near completed.
The more reliable, better cars and superior drivers normally stay on the track for longer, a short unexpected race distance won't reward them like it should. Therefore I don't think it would be right to award full points.
The teams also all knew with a good degree of accuracy that there was going to be a deluge of rain a certain number of laps into the race and this would more than likely mean that the race would be abandoned.
A team could even device their own race stategy accordingly so they were leading the race when this downpour occured, this would also be unfair.