The defence that you were just obeying orders is not in itself a valid defence against a finding of guilt, unless it can be demonstrated that the coercion involved was such as to mean that the act was not voluntary. It might be possible to argue that you genuinely did not appreciate that an act was illegal, because you had been misinformed by your superiors.   

"The basis of Western legal argument is innocent unless proven guilty". Precisely - and if it can be shown that someone has been coerced or suborned into pleading guilty, that means that plea should not be accepted. That does not mean they are not guilty, it means that whether they are guilty or not is still for a court to find.

I would have thought that, if in this case the court has determined that Ms England had been induced to enter a false plea of guilty, those responsible for doing this must be at risk of some kind of legal sanction, such as contempt of court.

And any army command which does not ensure that soldiers are aware of their duty to refuse to take part in atrocities, even when ordered to do so, carries a significant responsibility for the consequences of that failure.

That's how it is supposed to work. However...