All these agencies, from the CDC to the EPA, ATF, etc. should not be allowed to set policy. They only publish findings. The FBI should be enforcing the policies set by congress, not these agencies. Second to that, the FBI should not be adjusting their efforts based on the president. It should only be adjusted by policies set by congress.
For example, CDC would have published the covid outbreak numbers, they would have published the effectiveness of the vax, they would have published rate of transmission etc.
Then congress would review these findings and create bills/laws that would address these findings.
How do we change the operating procedures to match the above?
Is it related to the issue that Marjorie Taylor Greene is trying to fix?
Obviously the long drawn out approach is to campaign and get people to elect a congress willing to implement this approach to governing.