To me the argument is silly, because it's likely that the majority of the peleton isn't riding on bread and water alone.
Any rider that has had a title taken away from him over the last 60 years in the sport for doping, after the fact, can not leave us satisafied at all that the runner up is a totally clean "winner." Not only, in fact one would likely have to go back pretty deep in th field to find the pure one.
The question we need to be asking ourselves is that in a hypothetically clean field would Contador still be the winner? Or is his doping giving him an unfair edge over his doped competitors? Perhaps more fundimentally, then, is his a real talent above the others, or only the fruit of chemicals? These are also the same questions we should ask of any grand tour winner of late, especially over the last 20 years since EPO hit the peleton.
I have my own answer to this, however I leave it up to each to decide for himself.
While I'd like to see the sport be rid of doping as much as the next guy, the inescapable reality of the culture of the sport necessitates a different criteria to pass judgment, than the mere black and white one we currently have in an anti-doping system that is far, far, from perfect (which means there are still lots of dopers getting away with it frankly).
On the other hand, for the record, if the title is taken from him he is officially not the winner, however hypocritical that may or may not be. While everyone must accept the consequences of their own actions.