Whatever evil the CIA may have done was the result of orders from above.Those orders are classified or deniable, of course.
But the most important thing is the disregard of individual common sense and "agency" -- the concept of delegation, encompassing both authority and responsibility.
This was also the excuse at Nuremburg.
In that sense agency can not write off "evil deeds" as the result of orders from above. Indeed, we have but one final master, and no human order can be obeyed which violates His orders.