I don't remember Greenwald ever claiming or even giving off a vibe that he didn't think that Manning was the leaker; this is a media critique, like most of his work. Doesn't bode well for the next 1400 words.
This reads to me - perhaps incorrectly - like Greenwald is saying that Manning may have a valid legal defense for his actions, as a military whistleblower. If so, I think - again, perhaps incorrectly - that Greenwald is wrong, and that the Supreme Court has put tighter limits on military whistleblowers than on the general public (Parker v. Levy 417 US 733 (1974) http://scholar.google.com/scholar_case?case=7171415278006906...). Please note that I'm speculating on what the law actually is, not what it ought to be.
I've read every article Greenwald has ever written on Manning, and I've never seem him state that, or even imply that Manning is not guilty. About the furthest I've seen him go is imply that perhaps we should not presume him to be guilty before trial, and that we should treat him as a suspect, and not a convicted felon, until that point.
Greenwald does go into some detail about why he considers Manning to be a 'whistleblower' - a term with legal meaning, as used in eg 'Military Whistleblower Protection Act.' It certainly sounds like he's suggesting it would be a valid defense (as in, 'yes, I did those things but I am not guilty because I was acting as a whistleblower'). If not, what do you think he means?