Black budgets alone are enough to make them a rogue agent for all practical intents and purposes.

How do you audit an organization like the CIA without the CIA's cooperation? In order to audit the CIA you must first trust the CIA, but the purpose of the audit would be to establish trust in the first place.

Trust of the CIA cannot be bootstrapped. They cannot be audited without trust. Since we cannot trust them, it would be foolish to believe that they are subservient to us.

It's not like those giving the black budgets don't know what they get in return.

It might be like that. First, anyone approving a budget knows what they're told, but probably has the capacity for very little first-hand verification. Second, not all budgets are "given" - we've previously seen the CIA raise money independently to fund illegal operations.

Let's put it this way: the president, and the congress could squash that in a second if there was a will.

Plausibly. I'm not sure how we'd tell. And there being "a will" may be dependent on an understanding of what's going on whose absence could - in principle - persist indefinitely.