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.
the CIA is simply using this as a clever way to cover itself. They had employees engaged in a political operation against the administration, and they want to hide that involvement by claiming everything is "classified" when it comes time for a hearing in open court.
Its a nice setup - use the CIA to run part of your shadow government, because that agency can hide any revelation of the facts behind the "it's classified" shield. In the meantime, Wilson is at every cocktail party talking about it, the information is circulated in every DC news agency - and not a word is said about that.