I don't see a legitimate need for agencies like the DOE, USDA, and so forth to have SWAT teams or even gun toting agents when you know, there are whole federal agencies dedicated to LE. Such as the FBI. Got a problem that needs armed popo for a federal crime? Call the local FBI office.
For years now, I've been arguing (mainly over beers and wings) that a great deal of money could be saved by placing all federal criminal investigations in the hands of the FBI, Secret Service, and US Marshall's Serice. Yes, you would need to increase the budget of these agencies, to a degree, but you could save millions in the budget just by eliminating the duplication. With seemingly every federal agency having its own investigative and enforcement department, you are talking about hundreds of sworn officers and all of their weapons and equipment that could be removed from the budget.
As for the OP, I'll be interested to see how it all turns out. His lawsuit for a 4th Amendment violation could be groundbreaking legal precedent...or a quick settlement out of court for an undisclosed amount of cash...