As you recognize, the Commerce Clause argument is a bit of a distraction--at most, it tells you that the states, rather than the federal government, are the right level to regulate drugs. The states, moreover, are not governments of limited, enumerated powers. They have general police powers. And indeed, as originally conceived, the states' exercise of those powers was not even subject to the Constitution. It was only 20th-century Supreme Court cases, interpreting the effect of the Civil War era amendments, that determined that the Bill of Rights applied to the states by way of the 14th amendment.

States have the general powers to regulate both the public health and public morality. Regulation of socially-harmful vices was always understood to be within the scope of state regulatory power. Adultery, for example, was uniformly illegal in colonial America, because of the potential threat to the social order. There is nothing that suggests the Constitution intended to deprive states of that traditional power. (To the contrary, those powers are expressly reserved to the states.) Regulating the ingestion of psychoactive substances falls squarely within that power.

I happen to agree with you to a degree--I don't think the Commerce Clause permits the federal government to make drugs illegal. (Indeed, I think the whole scheme of federal systems for public health are constitutionally questionable, since that is something historically committed to the states.) But the state governments inherited all the powers of the British sovereign, save for those delegated to the federal government, and subject only to peoples' individual rights. While those individual rights aren't necessarily enumerated in the Constitution, they must exist and be recognized. Nobody has ever recognized a general right of individuals to "do what they want with their own bodies." Drug prohibition is fair game for the states.