none of what you have said explains the REASON why her status could not be part of the case.
the explantion you are asking us to accept is - "because the CIA said so". That's not a reason, its simply an acknowledgment of what other facts show to be, a totally arbitrary decision.
Give me a REASON why her status should be exlcuded from this case? Don't just tell me - "because the CIA says so". The CIA is infested with people who are pursuing other agendas.
CIPA is the 'classified information procedures act.' It sets forth the methods for dealing with classified information in a public setting like a trial. Her employment was dealt with in CIPA proceedings. The 'deal' struck by the parties and the judge came out of CIPA proceedings. The indictment itself says her employment with CIA was classified. If this were not the case, it is highly unlikely that it would be handled by the court in a CIPA hearing. You, apparently, believe that it is common for courts to hold CIPA hearings about information that is not classified. It isn't.
1 - Because it is classified.
2 - Because it is not material to any charge in the case.