There is a difference, if a rule is changed and therefore something that was legal before isn't now legal, that is one thing. If a rule always intended said thing to be illegal, but some idiot at some race randomly decides it is legal for a few races, before the same thing being declared illegal, that is a bit different.
Essentially what has happened here, from what I can tell is, the stewards/whiting have INCORRECTLY deemed something legal, that in fact wasn't.
What happens if HRT to grab some press just throw a turbo in their car, and Whiting has a funny weekend and decides its legal for no apparent reason, and a couple weeks later the FIA get together and say, errm, no thats illegal. Yes, that isn't going to happen but, what RBR did was illegal, it was always intended to be illegal, at a couple of races the guys scrutineering the card, not so much passed it, but to me mostly weren't 100% sure of the rule itself.
Once the rule was clarified, the passing of the cars for that race should also have been clarified. For me I guess the car passing the test at previous races should have come with a stipulation that, they aren't 100% sure on the rule, it will go to a FIA meeting and they will decide both the exact rule and if it passes.
In this case I think it comes down simply to a mistake by the people who ever passed it legal, I can't see how the points can stand to be honest, even worse is, did the advantage get them to the front of the grid, probably it did, in doing so they let Webber back the pack up to let Vettel(also in a car breaking the rules) to jump WAY ahead of where he should have been. So they cheated, got to the front, and used that to leapfrog Vettel way up the standings.
There are times when a rule is completely unclear, or simply something never considered in the rules, that is where the creativity comes in. This isn't that, this is a rule being almost completely clear, the intention clear but a team purposefully misinterpreting something to gain an advantage and a few races a car being incorrectly determined legal.
Double diffuser wasn't and shouldn't have been illegal, that was creative, extra holes in a place everyone wants them, not creative, simply classified as illegal already, but some bad stewarding/checking and they get to keep their points, that is a joke.