If a state tried to prosecute a federal agent for enforcing state law the agent could and would assert sovereign immunity. A state likely can't prosecute the federal government or it's agents(when acting within the scope of their duties) for a violation of state law. Idaho v. Horiuchi (ruby ridge case). (district court dismissed case, 9th circuit affirmed then reheard and reversed, and then was about to rehear the case again when Idaho dropped the charges)
I think in the case of a federal agent being arrested for simply enforcing federal law, it won't be as close of a call as Horiuchi.
The supremacy clause, sovereign immunity, and the supreme court's interpretation of the commerce clause in Raich renders this law nothing but symbolic.
The Constitution and Federal Law mean what the Supreme Court says they do. (Marbury v.s Madison) Until a federal law is held by a federal court to be unconstitutional it is the supreme law of the land.