No, McCarthy was a career CIA employee. She joined the Agency in 1984 as an analyst. Most of the NSC is comprised of career employees from State, DOD, CIA, and other agencies. Usually, the various agencies nominate people for these jobs. Their nominations are reviewed by the NSC Director and approved/disapproved. Even though McCarthy was in a political appointee position, i.e., the President could appoint whomever he wanted, she was still in the CIA.
You noted the "tricky" part, political appointees typically are NOT civil servant covered positions. Was she still a political appointee or civil servant when she became attached to the Center for Strategic & International Studies?