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Clearly the pills made for pharmaceutical are incredibly dangerous, even when taken as per the instructions. That is why they are prescribed."
Nope. Simplistic, backwards thinking.
There's nothing dangerous about taking a valium to help you sleep once in a while, unless you have a specific allergy. And that is what you would be instructed to do if you were suffering from insomnia or panic attacks.
They are controlled because they are dangerous in large amounts and addictive if used frequently.
Some antibiotics are controlled because people see them as a magic cure-all and would take them for everything, which would even more rapidly lead to resistant strains of bacteria and make the antibiotics useless.
So sure, some drugs are dangerous when used as instructed, but many are only dangerous when abused, and some have wider implications for society.