Personally I think Lemond is fine when he talks about the rise of EPO and its effects in the early 90’s. Clearly the EPO users got fast and there was indeed a peloton at two speeds, at least until everyone started using. When Lemond and others bemoan this I think they’re justified, because what they’re talking about is a change in ability across the entire peloton. The average rider got a lot faster, and while technology, training, and team support also improved I don’t think there’s any question that pharmaceuticals were the primary cause.
However, this is much different than looking at the performance of a single rider and calling them dirty, especially if that rider is the best in the peloton. Like everything else, rider ability is spread across a distribution and you can rarely say anything about the extremes of a distribution even if you can characterize the average. By definition, extreme cases like Contador are unlike anyone else in the population. They are literally in a class by themselves, so even if everyone they’re beating is doping it is impossible to know if they are as well (e.g. Armstrong in his prime). Unless they fail a test, of course. One would think that Greg Lemond, himself one of these extreme cases, would recognize this.
If we really did understand physiology to the extent Lemond thinks he does, then we could move past these statistical arguments. But the fact that statistics-based methods (epidemiology, statistical genetics) are still the source of most biomedical knowledge suggests otherwise.
So when Lemond rants about the general use of drugs in cycling he’s got a point, but when he demands that a specific rider justify their results he’s just being a nut.