So I've read most of this thread... it's very long. And it's not terribly dissimilar to one I was party too some months ago. That was about such things as Enghien and Amiens as well, and a bit of a wrestle about Napoleon being or not being a nice chap.
Weighing in here at this stage requires waders, but hey it's a discussion forum. Firstly let's throw this good guy bad guy Napoleon out the window. He was a statesman, who lead his country, this obliged him on certain occasions to act in ways contrary to most normal patterns of behaviour and ethics.
Most leaders wishing reform and I have no reason to doubt that Napoleon did not wish it, usually fall foul to pleasing their supporters and keeping themselves in power. This is common to all kinds of leaders, elected or unelected throughout history and the world.
What we should keep in mind is that the powers of the age, saw Napoleon as a threat to their rule, and also would not recognise him as a Bourbon replacement in France while heirs of that house still lived, without military force compelling them to do so.
The peace of Amiens broke down by a mutual distrust and posturing by France and Britain. Both acted and asked for things they knew the other could not accept. The death of Enghien was strictly speaking legal, but what is legal is not always right or just. As a royalist the Duc could not expect much mercy if he crossed the ruling power. The only charge that stuck was treason and bearing arms against France. Everything else including conspiracies to assassinate Napoleon cannot be proved.
The miscarriage of justice attending the act of violating sovereign soil to kidnap, hastily try and execute a public figure is indeed irretrievably tied up in the reason for the outcry. Enghien was not the first royalist to be executed by republicans after all. Despite the cynical nature of what has been put here regarding 18th and 19th century justice, military justice for deserters in the face of the enemy must be dismissed from this case as precedence. May I draw your attention to a case of soldiers aiding civil power in Boston in 1770; here soldiers and their officer. who opened fire on a crowd were brought before a civil court and tried fairly, defended by Mr. John Adams, thereafter acquitted some with minor penalties. Nor can corporal punishment enter the discussion because though the French did not flog, they did beat and again it's got nothing to do with the case in hand. Likewise although the laws back then were indeed harsh this does not mean to say everyone suspected of a Capitol crime met his or her end at the hands of a public executioner.
This is not the case of a soldier disobaying orders in the face of the enemy, otherwise treason and rebellion wouldn't really come into it, the charge would be mutiny or desertion. This is a matter of the state verses an individual. And the entire matter is deeply suspect in the manner Enghien was apprehended and tried. I say this not to blacken Napoleon's name, for it is true it is a delicate business to implicate him directly, and I for one have a more nuanced appreciation of Napoleon's foreign policy than some in this thread, yet can't be bothered to comment in terms of right and wrong and prefer in terms of scholarship an analytical approach.
Boiled all down, if I was to say, yes Enghien was tried fairly for crimes against the state, I would have to say that Ney and Bedoyere were tried fairly for treason against the Bourbons. Such is the tragedy of civil war I suppose.