I think it would be a terrible idea to change the system. Doing so could even conceivably punish a lesser team that, through strange circumstances manages to score great points in one race.
Lets say that conditions in Hungary hadlead to the elimination of both Bulls and one each from McLaren and Ferrari, and the two that weren't eliminated were damaged. So, if Lotus were, through those conditions, to score a 1-2, they would lose a large part of the benefit of their luck on that occassion. Not fair in my book, especially since money for the teams standing is involved!
If a team builds a dominant car, they should be allowed to reap the rewards in points.