It's not accepted, but that is not the point of discussion here, and in an event of a nuclear war there are more to worry about than a trial.
Also, there might be a difference between just following orders but being aware of the consequences of following such orders, versus following instructions in the blind. If you were told to pull a trigger in a room while in another room another person is shot without you being aware of it, are you still guilty of the crime? I won't offer an answer but suffice to say that you signed away a measure of moral/legal guarantees when you sign up for the armed forces. You are in effect short of selling your soul away to third party for the contracted period and you trust that he is not the devil or will not become one.
People sign up for the armed forces with their own thoughts of how things would be like but it does not matter, what matters is what those in control of said armed forces want to do, and once you signed up you are required to follow orders or face consequences, and if the order is 'wrong' you will still share some repercussions. Which is why it is said in the art of war that "Now the general is the bulwark of the State; if the bulwark is complete at all points; the State will be strong; if the bulwark is defective, the State will be weak." I would add that if the general is wrong, all that follows him would be wrong, hence victory is sometimes everything that an army strives for, and victory depends on setting the right goals, and knowing what can be attempted and what should not be.
Which raises another point namely that whether using nuclear weapons on civilian targets like large cities constitutes as war crime. If you are the victor I guess you could get away with it but it's unlikely that there would be a clear winner in a large scale nuclear exchange.