Technically, the CIA never flew the SR-71. They flew the A-12. Only the USAF and NASA has flown the SR-71. A-12 is a single aircraft. USAF wanted their own and wanted two seats; SR-71.

If CIA A-12 crews were killed, that wouldn't affect the USAF SR-71 stats. Further still, a quick poke around wikipedia shows that 12 SR-71's were destroyed in accidents, though none to enemy fire. Nothing mentioned in the article I read whether anyone was killed, though I believe if crews had been killed, it probably would have been mentioned.