These agencies are part of the executive and greenlit by the legislature. Mentally divorcing them from that is part of the problem and creates this exact situation where the agencies roam uncontrolled.

The chain of accountability for their actions does not end at the head of the agency. It extends into both the White House as well as Congress. As indeed "resignations here and there" are pointless, the public perception needs to shift to a point where elected officials are actually held to what they do (as opposed to, as is frequently happening, what they say.)