This is direct action. It isn't script kiddies, it isn't Anonymous, it isn't a random 1337_h4xr pulling off some minor corporate sting. It's the real deal, it's programmers putting their lifeblood into an endeavor that changed the fate of nations.
So whatever flaws that happened to exist don't change the inherent absolute confidence of the maneuver, nor does it change the precision you praise in your post.
But it also means that it can't be perfect. Anything that's so grounded in reality will not be perfect. That's the rules of playing the big games--you can't please everyone, you can't perform to the theoretical maximum that the weak articles that call it "nothing special after all" espouse.
Because that theoretical maximum was out of the reach of stuxnet's writers from the beginning, and they fucking dealt with it. People writing articles now have had nothing to do with crippling Iran's nuclear capability, if even for a moment, and the hogwash in the blogosphere that exists is so much shallow posturing.