These people are in for a world of hurt, the State Department tells the CIA what to do.
Your broader point is correct, but no, it doesn't. The CIA is an independent agency [1]. It reports to the DNI [2].
[1] https://en.wikipedia.org/wiki/Independent_agencies_of_the_Un...
[2] https://en.wikipedia.org/wiki/Director_of_National_Intellige...
The Director and Deputy Director of the CIA.