Well, I think there are so many things in this world that don't follow that statement. People decide to take drugs because they like them, they don't do it because of what it may do to them health-wise. So ultimately, the punishment associated with it should not be health related. If the punishment was less severe, then the usage would become more world-wide. Ie... if a drug was still illegal, but with a more basic punishment, then more people would be likely to do it, ultimately causing exactly what they don't want.
I mean... for the honor system on a train. If you get caught without a ticket, they don't fine you for just the ticket that you ~should~ have bought. They make the fine so large, that it deters people from doing it. And also, if someone does do it, the will assume that it's happened before.
So in terms of logistics? I don't really agree. I think the system wouldn't work. I assume your mainly referencing marijuana and the fact that there hasn't been any solid proof that it does not cause any major health problems... but there's a difference between altering the "punishment" and removing it completely.
Of course, then it comes to things like cigarettes, which is completely legal, even though many would easily be able to prove that a cigarette is more damaging than marijuana would be.
Ultimately, punishments are always "worse" than the crime, at least from the individual's person's standpoint, and that's because if it WASN'T worse, then many people would more likely opt taking the risk....
Hopefully that makes sense.