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?
Career employees can fill political appointee jobs. It is quite common. Check out my link to the Plum book in #151. Ambassadorships are a good example.
Was she still a political appointee or civil servant when she became attached to the Center for Strategic & International Studies?
She was a civil servant on a sabbatical from the Agency, which means usually LWOP. Without knowing specifically how it was handled, there could be two scenarios. One, she could have been on a LWOP with CSIS picking up her salary costs. She would not receive credit for her USG pension. Two, the Agnecy paid her salary and loaned her to CSIS believing that it aided her professional development.
I would note that McCarthy was on the verge of retirement in 2006, which would have given her 22 years service with the CSIS service credited. She would need at least 20 years and be over age 55 to start receiving her pension immediately.