I agree that the war on drugs is stupid and causes more harm than good. However, the counter argument that "people should be allowed to do things that only hurts themselves" is pretty poor in the case of most addictions (including but definitely not limited to drugs).
The question is whether jail is an environment that will make them better people and help them overcome these problems. A related question is whether armed police, not doctors/therapists, should be the ones we send to deal with people who have not used fraud or violence against another person.
Unfortunately, most people only think of the immediate physical effects (e.g. secondhand smoke) and don't think of the more long-term effects, especially those which are harder to quantify.
It's hard to think of a more damaging long-term effect than expanding the definition of "crime" to include "something other than using force/fraud to harm another human being", the subsequent mutilation of the Fourth Amendment, the asset forfeiture abuses that continue to happen, and the increasingly aggressive paramilitary police that even the law-abiding are afraid of. Ask an older person about what police used to be like sometime.