He's getting a lot of support he doesn't deserve. A soldier DOES have the right, the responsibility, to question orders. We didn't accept the excuse for Nazis, and we don't accept that excuse when our own take part in crimes against humanity.
BUT... that isn't what happened here. Watada decided he wasn't going AT ALL. Once there, he could have taken a stand as to the direct orders he was given. If he has been ordered to kill wrongly, or fire indiscriminately, or anything he considered to be a war crime he could have taken his lumps and refused and been where he is today with a LOT more support.
Instead, he knew that his life was threatened just by being there. Not his moral standing, or his integrity as a soldier, his life. That's one thing that soldiers don't have the legal right to question orders about, because if they did every single military operation would end up being a deadlocked debate of the military's plan.