Tennyson put it best in "Charge of the Light Brigade"
'Their's not to reason why, theirs but to do and die.' That is 19th Century. When people believe their government knew what it was doing. After Crimea, WW1, WW2, Vietnam, Bosnia, Croatia etc showed that sometimes to obey orders is not good enough as reasons to slaughter and massacre.
In Vietnam, a French general said something similar, if not as much talented tha Tennyson lines: "Legionnaires, you are here to die. I sent you where you will die"
Now, in this case, yes, he could have resigned… We had same kind of case in France during the 1st Gulf War. Helicopters’ pilot who refused to be deployed saying they didn’t join the army “for that”, meaning going to war. They wanted to get the training, the money but not to do the job…
Well, they were not shot dead, even if the war was legal, voted by the French Parliament. They just had to find another job, and are barred to any official job.