Things have shifted because they've had to. The CIA is in the business of clandestine operations, strongly preferring to support an existing entity and failing that, small operations with extreme amounts of plausible deniability. For one, JA is just the messenger (as you point out, BM is the one who leaked the cables, and that damage has already been done), and JA is/was not even all of WL (although don't tell that to JA..). but really, since he's made it into the public spotlight, direct action is out of the question and JA can only be taken down through an illusion of law and process.