If we do ever manage to address the interstate commerce clause, we'll have to account for the fact that our day to day functioning has come to depend on a number of large federal regulatory bodies whose legitimacy is derived from it (ex FDA, FCC, etc).
The simplest way to deal with that would be to have those bodies continue to exist and publish "suggested" rules, which all the states could then adopt wholesale if they don't want to be bothered to do anything different.
Or a state could do something different, if they wanted to, which is kind of the point.
When the CDC recommends action for workplace safety in light of a strain E. Coli found in a crop grown in one state and sold in many, state health departments and state labor departments have full autonomy on how to handle the issue in their respective states.
If anything, the problem is that when there are no rules, some people (pilots) themselves were reckless and can endanger others. That is something to be solved by criminal courts, though.