Great question; I think a major reason many who dope are able to rationalize their behavior is because we have dogmatically just maintained that "doping is bad" without really establishing a well-thought out basis for it.
Sure, the argument for doping control that seems to predominate is a paternalist one. (At least this is better than the worst argument I've ever heard for doping control, which is "them's the rules, live by them"). By banning doping, WADA - or whoever - is watching out for the athletes' health (AND the health of kids that emulate those athletes). Further, injecting, injesting, or smearing strange chemicals is bad for you. And we can't be trusted to keep from hurting ourselves by using them. Fair enough. BUT 1) not all the banned drugs have terrible side effects- long or short term, if used, um, "properly" (a la Ritalin, arguably EPO). In fact, the debate about Ritalin "abuse" is raging in the medical community. Because there is little evidence it's abuse is actually "bad" for you, some are saying we should let anyone and everyone use it.
And 2) we do a ton of stuff to ourselves besides doping that have horrendous long term effects. let's ignore the harmful effects of legal supplements. Besides that, training 130+ miles a week is not "good" for you, I think most doctors would agree to that. Going on a 70% fat diet (as one European training group did) is not "good" for you. Doing a gut busting workout in 110 degree heat that screws up your hypothalamus is not "good" for you. But these things are not banned, or controlled in any fashion. We actually ADMIRE this behavior.
In the end, I think if you are going to sing the paternalist tune about protecting health (in my opinion, there are better ways to argue for doping control, but...), the best you can do is say that our attempts to protect athlete health are noble, but incomplete. We can't stop athletes from ALL the bad things they do to themselves, but this is one thing that we have a decent chance of actually controlling.
That is, we can't watch every athlete everywhere to make sure they are not training in 110 degree heat, say. Runners don't have odometers on their legs that tell us how many miles they ran in a week. But it is accurate/easy/reasonably cheap to run laboratory tests to see if athletes have dangerous chemicals in their system. (Counter argument: our doping control is 1) not that cheap, and 2) not that easy, and 3) not that accurate)
Sorry for the long post, I just think this is an important issue to talk about. Bump.