I'm not very much interested in attacking the Steroid era of baseball. My approach is to let all players do whatever they can to maximize their physical performance. They are the ones who will be held accountable for any health problems later, and if everyone has an equal chance to use any substance then it would be fair for all of them.
Yet, the reality is steroids are illegal to distribute (and use?) without a medical reason. Also, right now steroids are banned substances, as are other enhancers. Some of them are presently either undetectable or difficult to determine.
Therefore if the sports leagues are serious, especially MLB, every year collect urine and blood samples from all players at random times. While some substances may be transparent to testing today, they won't always be. Even if the cheaters are ahead of the scientists today, the enforcers will catch up eventually. So the answer is that players will be held responsible for using banned substances whenever they are caught. They will have to forfeit substantial sums of money whenever they are caught.
The league should force players to set aside a certain amount of money to be forfeited if they are found to be cheating. In addition, they could require players have "banned substance" insurance which would be used to pay back Major League Baseball if the player is ever found to have cheated. This way even if it's 15 years from now, there will still be a punishment. Also, the premium charged for the insurance would represent the risk to the insurance company that the player is actually honest and not doing anything wrong. If this is done honestly, and made public there would be a detterent to cheating right there.
Right now Human Growth Hormones apparently are only detectable through blood tests (which aren't allowed). The owners should take a hard line and demand that any test that passes scientific approval is allowed to be used on current and past samples. Any substance that is proven to enhance is subject to punishment whether it is generally known today or not.
Remember this is not for the purpose of incarceration but for cleaning up a game where the players have taken out to cheat the system.
I would change the system, but if not then enforce the rules in a way that will end this discussion rather quickly.