"If the results of professional regulating bodies and the years of inquiries are going to be discarded, then why have them in the first place?"
See, works like that too.
Listen: I know you (/the OP) love a nice feel-good hero story, and Armstrong was a made-for-TV one. But just a few things:
1) Armstrong gave up his rights to challenge the accusations of the USADA and lost all his legal challenges to their jurisdiction over the matter: he is guilty, end of story.
It does not matter whether you are "tired" of fighting accusations or whatever other excuses he could find: if you waive your right to present your case and challenge the accusations, you are implicitly admitting guilt. The USADA is not some Soviets-era corrupt body out to get him (as backed by a couple court decisions against Armstrong claims).
2) For a laugh, have a look at the many articles (have only seen some in French and German, but I'm sure English versions will pop up) that go over what the "revised" winners would be for all the Tour de France titles he might be stripped of: if you eliminate all the other riders who have since been convicted of doping, the actual winner is on average fourth or fifth in the ranking at the time (in one case, all up to the *9th* have been eliminated since).
While the fact that doping is widespread is nothing new, and does not prove in itself that Armstrong did it, think about it for a second: this means that he consistently beat between 3 and 7 people who *were* using doping products. Yea... I guess he was that good.
3) As shown above, doping is rarely detected during the races, but sometimes takes years to come up: sometimes by applying newer scientific methods to older samples, most often by uncovering doping networks (crooked doctors providing the products etc) and identifying the people tied to them. Many of the techniques Armstrong is accused of using (such as transfusions) are extremely difficult to detect, if at all. In such cases, it is perfectly valid to use testimonies.
4) Within the case built by the USADA against him, is a mention of his close relationship with the UCI (as one of their most generous donator) and personal friendship with its president. All things concurring to explain why he may have benefitted from some warnings ahead of tests, as well as unusual leniency when he failed to submit to testing.
5) Despite all that,
there *were* two cases where Armstrong did test positive for doping substances. While he successfully (and not very convincingly) fought the first instance (1999), the second one (2005) is still very much outstanding and has not been disproven nor confirmed (due to the "unfortunate" lack of a duplicate sample).
So, yea, Science(tm)