I was only following orders is not an argument that works. Look at Abu ghraib. Military Intelligence and JAG reviewed the processes and let them proceed. I agree, there are repercussions for your actions. But those come with due process. Those come with a trial and a review of the situation. Not from a megalomaniac that is mad that you didn't blindly follow his word.
But you can't just resign from the military. You're stuck and have to make the most of a bad situation. But Yates was free to resign.