I'm actually in agreement with you here, but I can see the other side. You have a substance that you know, for a fact, a certain proportion of the population will abuse, to the detriment of both themselves and society at large. If you make it illegal, the proportion who fall to its ill effects may be reduced, even if the cost to those who still use it is greatly magnified. It's a classic case of what's best for society versus what's best for the individual.
I, personally, would argue that enforcing overly harsh rules results in a net cost for society, due to the costs of enforcement, loss of productivity to society by those you put in jail, etc. But the motive behind these laws is not always just "muh morality," and it's not a sure bet that allowing people unfettered freedom in their personal life is a good thing for society.