I seem to recall most of the lower level nazis put on trial getting away with the argument that they were just following orders, and to refuse would have left them dead. It was only those who were of either political importance or behind the orders in the first place who didn't get away with it. Which is as it should be.
Soldiers are pieces of a machine, and they cannot question what the machine is doing. As much as you like arguing "The machine is evil and bottom-rung soldiers are obviously better equipped to deal with the complex moral clusterfuck that is war than officers because... uh... they're not part of the machine, man... or something...", what about when the soldiers come to conclusions you don't like? Think of the squad that made a game of killing civilians that wound up court marshaled when someone else in the platoon ratted them out to a higher officer (note that if they must break normal procedure to reveal blatant wrongdoing, going up their own damn ladder is the way to do it; still frowned upon, but not, you know, treason). That was also a case of soldiers thinking for themselves, and drawing their own conclusions. How about the soldiers that snap and start shooting their comrades? Thinking for themselves. While the Manning case is rather mild, especially compared to those, it is only so because of the general unimportance of everything leaked; he accomplished nothing of value, and left his head on the chopping block.
Doctors are a special case, being highly educated individuals whose very job requires them to draw conclusions in radically varying situations, and who are oathbound to a specific code of ethics. A doctor endangering the life of a patient over a petty grudge is a dire offense. A soldier (well, specifically a low-level grunt) is, by virtue of not being an officer, not in possession of the skills to make such sweeping decisions about what is right or wrong in regards to their orders, and privy to only the smallest part of the overall picture to boot. They're entitled to their opinions, they're not entitled to act upon them. You're trying to hold up one individual as why soldiers should think for themselves, and ignoring all the cases where that leads to them committing crimes and atrocities, because that's what they decide is best.