In an earlier post on this subject I wondered if the statement purportedly from the Taliban taking credit for the murder was genuine. This story reveals that the assassin was a CIA guy, but suggests that he had been recruited by the Taliban. This is, in my view, quite unlikely. First, only the most trusted are allowed to fill a security position where he/she could get close enough to assassinate the "client." Secondly, these people are closely monitored for any signs of disaffection, let alone defection. The erratic behavior described by the victim's brother, if it occurred, would have caused alarms to go off.
This article leads me to think that Karzai's assassination was the Agency doing a little housekeeping. I'm not yet convinced, but it's now the working hypothesis.
http://www.informationclearinghouse.info/article28606.htm