Ugh, I had a well thought-out post that apparently got eaten when the site went down. Now I'm disenchanted and can't be arsed to type it all again.
Knowing several people in the military, and considering joining the Air Force in both regular and National Guard flavors, I spend a little time on this subject.
Basically, the grunts that run into obviously "morally questionable" orders have three options, once they reach their breaking point... which usually happens between the first time they see a civilian death they acknowledge was needless and their third tour.
1. Ignore or disobey the order. Not only will this accomplish nothing, as they'll just find someone else to carry out the order as your replacement, but you'll be shipped off to jail. And not the good kind of jail, either.
Fort Leavenworth jail. If you thought the orders you were being forced to follow were horrible, you're mistaken. I've seen some of those "corrections specialists" that come from/aspire to go to Fort Leonard Wood; you don't want to meet them, let alone be at their mercy.
2. Put your blinders on and your head down, and do whatever your CO says. Most of these people are the ones that still think Saddam had something to do with 9/11, rationalized unjust things happening to them (see: dropped into a war zone with no body armor), and generally just eagerly take any order given to them for any reason they're given. These are the same people that either fall apart when they get out of the service and don't have an immediate authoritative figure dictating their lives anymore ("Brooks was here"), or end up being enlisted for thirty years because they don't know any different but can't give any orders.
3. Desert to another country, and hope they're nice to you.