Even if physical evidence is missing, not even Armstrong's most ardent supporters could dismiss George Hincapie's damning, and self-implicating, testimony.
The outcome would be truly shocking, but for the fact that it was pretty damn obvious to anyone following cycling in the 1990s that nearly everyone was doping. Would Armstrong have one one, let alone seven consecutive, Tours de France had he not doped? Certainly not, simply because all of his chief competitors were engaged in the same kind of systematic doping programs that his team employed. In my view, he prevailed on a pretty level playing field. Who knows what might have happened if no one had been doping. Perhaps Armstrong still would have prevailed seven straight times. But we'll never know.
Finally, like several of his toughest competitors (such as Jan Ulrich), Armstrong was a tremendous athlete and cyclist, who trained tens of thousands of miles a year on the bike (some of which was facilitated by the use of banned substances that may have prevented or ameliorated injuries and fatigue). The edge he gained by using performance-enhancing drugs was only marginal, as was the case for other great Tour de France legends going back to the earliest days of the contest, when riders used cocaine to prevent fatigue and dull pain (see here).
The total level of doping in cycling is probably lower today than during Armstrong's era (and maybe ever), but that is not to say that cyclists no longer seek an edge. The positive incentives to dope are all still there, including the money, the fame, the amount of competition, and the sheer bio-physical difficulty of riding long stage races (including back-to-back-to-back mountain stages). All that is holding them back are technological advances and greater intensity in monitoring and detection. Meanwhile, because of the structure of incentives, there is every reason to expect continued improvements in technologies to avoid or defeat detection.
Finally, whatever the effect of the doping scandal on Lance Armstrong's reputation as a cyclist (I personally believe the long-term effect will be negligible), he is and will remain a hero to millions of cancer sufferers and survivors.