I'm a bit confused by your post and would like to understand you thoughts on these lines.

Several studies have been published on the topic of why the South lost. Just two thoughts along those lines --

1) The American Colonies won the Revolutionary War in large part due to military intervention by a powerful foreign ally. Without French assistance, the colonies probably would have been defeated as the Confederate states were.

2) If the Americans had lost the Revolution, would we think of the rebels in much the same way as we do the Confederates -- misguided romantics who brought misfortune upon themselves (it's good that they lost)?

I don't understand the connection you've made between the Confederacy's treatment of deserters, and "the whole idea of an independent confederacy of states" being something you would oppose.

During time of war the governments of most countries would sanction execution of deseters. U.S. military code does not treat desertion lightly -- if a deserter is caught, he can expect real trouble. Does that alone make the U.S. government something you would oppose.