I haven't seen this anywhere yet, so I'll suggest it as an alternative line of thinking.
Suppose Khan was not an agent. Suppose he was never captured in Pakistan and was never convinced to be a double agent and pass internal AQ communications to the ISI and CIA. Suppose he was never "outed" by some Whitehouse official trying to shore up the Orange Alert?
Suppose this is all one big, multinational black propaganda psychwar against AQ.
Originally a comment on this thread.
I haven't seen this anywhere yet, so I'll suggest it as an alternative line of thinking.
Suppose Khan was not an agent. Suppose we knew his position in the organization and his importance to AQ, but we couldn't actually catch him. By leaking that he is a double agent we threaten his credibility within AQ. By creating an uproar about his outing we confirm it as truth (e.g. annoyed intel officials from various countries muttering about how his name shouldn't have been made public).
The radio man for AQ is now an untouchable for any AQ operative. They think he's been turned, but they aren't sure, and it's not worth the risk. All of Khan's friends stop calling and emailing. Everyone changes their email address. Communications are disrupted and operations are put on hold.
It's not as good as having a man forwarding the email list to Langley, but it's still pretty damn good result. Especially for a lie.
REF: PRO·PA·GAN·DA: a primer for identification at www.kuro5hin.org