I'm not sure what you mean Natalie. Soldiers are many times ordered to do things by their commanders. Much more than in real life their decisions have to be immediate and any insubordination can mean a court marshal and in the past even execution. Still, soldiers are expected to defy commands when they are unreasonable. Not merely unlawful commands, soldiers in the German army could be prosecuted even for fulfilling the commands of the administration. I don't think his comment provides much of a shield for them and is more his way of avoiding the situation. They tried a similar trick with the AIG bonuses. The law is very important for the American public and they use this to try to avoid criticism. If it works great, and if not it was still worth the try.
Politically it is very easy to engage with the gap by simply not accepting it. In war you are told many times to kill people. Still, if you just go and murder for no reason you can be tried and thus they can be tried as torutring someone illegaly, not accepting the mandate they got as legally binding.
But, and it is a big but, if you accept this argument, what happens with Bush and his whole cabinet. Unless you are willing to put them under trial, and I just don't think the american public is up for it, then you can't try to throw it only on the person who did the torturing. There is no question how high this goes and unless you are willing to go high it simply won't stand in court as the next step is clear. It was all too out in the open. Perhaps that's what Obama meant by what he said.
(But also, the tortures in Abu Ghraib seemed to have very little point
to them, something which might help the prosecution case. Whatever one
thinks of the necessity of torture in certain cases, meaningless
torture is not easy to accept as legal in any real sense. Though even in this case how high do you go...)
As a side point: though I'm a big admirer of Errol Morris' films, I disagree with his quote. I think people take pictures today to know that they live, that they exist, and it doesn't mean anything like that "they never fully accepted what was happening as normal". I didn't see the movie but I will try to