How do you ever clean up a corrupt organization? Management 101

It's a basic principle of management that good managers select the best people for key positions.

Conversely, incompetent or corrupt managers almost always put incompetent or corrupt people in key positions, since it makes it far less likely that the top exec's incompetence or corruption will be revealed by a subordinate. 

Honest, competent employees eventually recognize this and leave, as they know people who blow the whistle on either corruption or incompetence are almost always fired. 

By huge contrast, while incompetent low-level employees also recognize what's happening, they realize that the way to promotion is to support the corruption or fail to call out the incompetence.  So they stay with the organization, agency or company.  Which makes things worse.

The inevitable result is that any organization that by misfortune gets a corrupt leader will inevitably be corrupted from top to bottom.

So...when an agency or company is shown to be rotten, you rarely fix it by firing just one or two top bosses, because their assistants--who would usually be chosen to replace them--are also corrupt.  So if you want to reform the organization you typically have to fire at least the top 25 or 30 percent to have any shot at cleaning out the carefully-chosen bad employees.

Looking at the FBI here, and DOJ, and probably CIA (due to Brennan proteges) and NSA.