I agree, pharma distribution is nationwide so federal oversight seems reasonable.
The point you address is one that is often misunderstood. When most people say the federal government should not be involved in activity X they often mean that a more local level of government should be involved. I other words a level that is (1) more knowledgable of the local environment that activity X is taking place in and (2) is more accountable to local voters.
With respect to (1) in particular, many problems have a local component. A good solution in one part of the country may be a poor solution in another. That is why many people are highly skeptical of one-size-fits-all solutions from Washington DC.
For EU readers, consider an EU based organization usurping control over some activity from your national government. That's sort of the situation with the US federal government. The US is too large and too diverse for many on-size-fits-all solutions.
OP is not a troll, and while I do tend to think that the FDA likely has a place under the interstate commerce clause I am willing to take the OPs position also.
The Constitution is a regulative document, not a normative document. We know it is a regulative document because of the 10th Amendment:
The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.
Normative: whatever is not prohibited in the document is permitted in practice
Regulative: should include those and only those powers, departments and responsibilities that are instituted, commanded, or appointed by command or example should be the purview of the Federal Government, all else is to the States, Municipalities / People