You know, I'm thinking maybe the CIA thought that Haladki went on the lam after he was revealed as the mole at the end of last season, so he was listed as missing rather than dead. But nothing's been explained.
When Jack was confronted by Will, he immediately went to Devlin. The breach must have come from within the CIA because it was CIA technology (the bug/pin) that was used to identify and contact Will. Further, the informant knew things only the CIA or SD-6 would know (such as the identity of Will's attacker). Jack pointed the finger at Haladki immediately (seeing him as disgruntled, and unhappy with the way the Prophecy incident worked out), but Devlin shut him down (and, oddly, put Haladki on the mole-hunt, which surpasseth understanding).