My point is simple, which you don't seem to get, apparently thinking it more complex:  they are not subject to the military justice system and Manning is, by his own choice when he volunteered and signed up and took the oath.

The military is a branch of the government. Yes, they are the ones who have jurisdiction over soldiers but they do not get to define what is and what is not treason. If a soldier commits treason, or any other crime, the military has first shot at convicting him, but if you or I commit treason it will still be some branch of government which has jurisdiction to prosecute us and it will still not be the case that that branch of government has the right to define treason on an ad hoc basis. It appears though that, even though they do not have that right, that they do, indeed, have the power. That is, if there is no counter-force which inhibits them. A specific particular act, either is or is not treason, but whether or not a person is in the military does not alter those two possibilities one iota.

Here comes the re-hash. Greenwald does not believe that Manning committed treason. He and I both think there are many other important aspects to his case but in the article quoted he focuses almost entirely on demonstrating that if Manning's actions constituted treason then so would those of Woodward and countless other journalists, politicians, and various other government operatives.  
 Treason is what Manning is charged with. Treason is the wrong charge unless treason can be arbitrarily defined on an ad hoc basis. If an arbitrary decision can be made that in this case the releasing of secrets was treason, then Greenwald's reasoning holds true, IMO. Woodward and countless others have passed on secret information. If that is treason then there is a government entity which could convict them of it.
The wrong charge is far from the only thing wrong in this case but it is the one narrower part that Greenwald examined and drew a conclusion about and it was that conclusion that you disagreed with.

Bradley Manning knew that when he signed up, he may be learning, among other things, to kill and maim people, and that he could be doing so under orders from commanders who he must not question. Somewhere afterwards along the line he changed his mind about what he signed up for.

Now we have turned to a different discussion than whether Greenwald was wrong in comparing Manning's actions to Woodwards'.  Manning knew that he might have to kill or maim under orders he must not question? I expect that you didn't give that one much thought. It is wrong under any philosophical system of value judgment I know of and is also against the letter and spirit of the Military Code of Conduct.  

At the same time, I think if all soldiers decided they should follow their own moral intuition in every circumstance when they didn't agree with the commands of the military institution to which they had sworn obedience, what kind of military would that be?

Surely you recognize that there are times when it is a correct moral decision to disobey an order and that disobedience should be recognized as being within the law even if not at the very base level.  At My Lai, who acted correctly, within the law, and within the bounds of morality, the soldiers who followed orders and killed the people in the ditch or the helicopter pilot who threatened to fire on the American troops if they didn't halt the carnage? So, if there is no one showing courage to act right I think I know what kind of military it would be, "I think that would be one where the soldiers who felt their commanders weren't killing enough Taliban sympathizers or Vietcong sympathizers would feel free to take it upon themselves to rectify the situation."


 None of this is meant to imply commentary on his treatment by what I see as a bunch of stupid idiots in charge at the Quantico brig, and I think that Judge Lind should have been much tougher on them for the Navy's own good.

The actions of those idiots at Quantico was quite public. Those idiots were good soldiers, or rather Marines in this case, and would have acted instantly to obey their Commander in Chief's orders if he had ordered them to act differently. But that too is broadening the subject. And, how was Judge Lind hard on them one tiny bit? Do you think their feelings are hurt, maybe? Is there any reason to expect that anyones military career was damaged? I agree that some toughness that hit upon the idiots at Quantico [I first typed "Guantanamo". Ironically similar.] might have been beneficial to the Navy. And to other branches. And to the country.