Nobody here, as far as I can understand, is actually questioning that the UCMJ had jurisdiction so while your understanding there is appreciated, it was never really in question...
The issue is a conflation of legality and morality. Conflating the two, then asserting that civilians may not understand and are unequipped to discuss the two separately, is toxic to discussion and society as a whole. It is an attempt to remove civilians from the discussion, a discussion that they absolutely must be apart of.
As much as some people may wish it, this ain't Starship Troopers.
It's a little obnoxious to be accused of conflating things one has explicitly separated, but I suppose on this topic those that are outraged are mainly here to vent rather than discuss, and there's nothing wrong with that, so I think I'll bow out here.
In an immoral legal system, justice is fleeting. He is accusing them of, not 'not existing', nor being incorrect, but rather of rendering a verdict that deserves no respect.
That's how I read it anyway.
Edit: His (much later) comment here (https://news.ycombinator.com/item?id=6251625) indicates to me that he understands this situation just fine. "I'm not disputing that Manning broke the laws of the military.... ...I don't see how you can defend the laws and regulations of an organization...."
The function of civil authority, say a moral President, something I hope to live to see, would be to pardon Manning, overruling the military justice sentence in the context of a greater good.
Clearly, this will not happen. Obama will simply wash his hands - not explicitly, though. The media will never even ask the question.
..but the more extreme "It TAKES a civilian mind to understand the difference between right and wrong" is also true? If the military is unable to consider morality itself, then we must rely on civilians to call them out. Accusing civilians of being incapable of doing that then puts the military above any sense of morality. Disturbing, to say the least.
That is what he was doing (see for clarification: https://news.ycombinator.com/item?id=6251625(, and that is why a reply of "civilians may not understand" got a strongly negative response.
It must be possible to understand that what Manning did was both the right thing to do and a clear violation of the armed forces code he agreed to uphold. Unlike civilian law, the armed forces must place a premium on obedience. People volunteer for and agree to these rules, so the outrage isn't as warranted.