Moloch:
Well, following orders is supposed to take precedence. There is always the chance that the officer has extra information.
I think it is always the soldiers responsibility to follow orders no matter what. EVEN if it becomes apparent that the orders were bullshit or evil - the soldier will still be reprimanded. They sure as hell can't get rewarded.
McCloud and the others will still get in trouble for not following Portia's orders earlier.
That depends on what legal/rational arguments you think society is following. According to the Nuremberg Trials of Nazi war criminals, soldiers have a moral obligation to disobey orders that they are aware would violate international law and human rights- such as executing unarmed civilians and engaging in slave labor practices. 'I was just following orders' is, under this mindset, an unacceptable argument in an circumstance.
However, legal systems that do not define the world as we do in modern, Western civilization might disagree with that. The Coalition States likely would deem that disobeying orders is a far greater crime then- for example- shooting a fleeing group of unarmed D-Bees. Whether Tolkeen would view things the same way, and for what reasons they would, could define a great deal of their national/military character.
They could argue that in a moral quandry, soldiers which refuse to take a questionable action are laudable- Lazlo would take this tact, as would the International Court in The Hague. They may, like the CS, say that obedience and discipline are desirable. While these soldiers are good people, following their moral instincts, they're likely not cut out for the military life and should be quickly removed from the service (dishonorably) before they damage unit moral and ultimately the mission. Tolkeen is also in the position to argue that, where their force is largely volunteer, largely self trained, and largely mercenary, they have almost no centralized authority over what an individual soldier does and thus, they can hold no one accountable for actions on moral grounds- right or wrong. As the only force in North America with the power to question Tolkeen's military practices (the CS) has already declared open war on them, it would be basically impossible for them to suffer for this approach on an international scale (Lazlo might take offense, but there's not much they can do to demand Tolkeen take moral positions on their actions other then write a sternly worded letter and maybe deny Tolkeen some required trade).
I believe the third approach is most in Tolkeen's character- they're generally disorganized and ready to ascribe blame for their actions on others, and far from moral paragons- but the call is really the GM's to make. But whatever call is made, it is important enough to answer a lot of questions about who and what the characters are fighting for (and against, in my case).
Wow, that got long fast.