A way to eliminate a federal agency:
1. Continue to pay the salaries of the employees.
2. Eliminate their authority to spend money.
3. Eliminate their authority to make any new regulations.
4. Put a hiring freeze in place.
5. Retire all federal employees (not the military) at 20 years.
The current employees could not complain about being fired. They would not get the satisfaction of giving money to their friends. They could not boss people around. As they retire, they are not replaced.
As the number of employees decreases, move them in with other agencies and sell their old office buildings. Within two terms, you would be able to completely shut down the targeted agencies.