The current administration's policy is that the problem is 'extremism', rather than any particular worldview (such as Islam, the Taliban, etc). This reluctance to name the enemy allows the enemy to flourish, which we understand to be the actual policy.
Perhaps on the grand scale, the CIA carefully obeys the POTUS, but as long as they have “plausible deniability”, and do not keep incriminating records, to a great extent they can have a free hand. Assuming, of course, that they are motivated to attack our national enemies.
If they are mistreated or undermined, they are far more likely to obey the (incomprehensible) book of rules, and do little or nothing unless they are micromanaged through it by their administrative oppressors, while keeping very detailed records that incriminate their bosses.