Pharmacies as intermediaries are probably a good idea, but only if they're required to deal face to face with the buyer or buyer's agent. Online purchasing is just like off-the-shelf purchasing, and does nothing to keep potentially dangerous drugs from being purchased by minors. Of course, right now, nothing stops a 10 year old from buying and taking all the acetaminophen s/he wants, right off the shelf, despite the fact that it's the leading cause of acute liver failure in the U.S., often necessitating liver transplants.
As for the FDA, I think it can serve as useful purpose as a certifying agency, but don't think it should have authority to keep any drug off the market. They should be able to say, we don't endorse Drug X, due to concern that its risks outweigh it benefits, but they should not be able to say that Drug X can't legally be sold to the public.
Something akin to the FDA would be needed to determine which few drugs really do need to be limited to prescription sales. Realistically, many things with risk-to-others levels comparable to alcohol simply won't be allowed on the market on a non-prescription basis, and there are certainly things with high potential for criminal misuse (e.g. Rohypnol) that any reasonable person would agree need to be tightly controlled.
I agree with your statement about the FDA as a certifying agency, however, a private agency could do this just as well and probably one would form due to demand by the public.
I disagree that some drugs need to be limited to perscription only. This opens the door to the type of tyranny we are currently living under.