I think it makes sense. What if it had been Alonso leading the race and then he piled into Weber's wreckage? Were there any flags out? If there weren't, I don't think he's at fault in the crash and would not deserve to have the race taken away.
Worst case, suppose that some tropical monsoon comes up and takes out every car except for a lone Minardi that has been in the pit for three laps getting a new steering wheel and nose cone or whatever. He comes out of the pit and crosses the finish line, does he desreve to win the race?
Anyway, I think it makes sense to use the pre-mayhem standings to determine the winner.