But under all circumstances torture of prisoners is criminal.

If those accused can prove that they were acting under orders when they carried out illegal actions, this is a mitigating circumstance, which could justify reduced penalties - but it is not in any way a defence against a finding of "guilty". There is a legal duty to refuse an illegal order.

Similarly, if it can be demonstarated that someone in a chain of command knew that illegal activities were being carried out by subordinates, even if they had not given orders for those actions, there is a duty to act to stop this happening. Failure to do so is, I believe, equivalent in law to actually ordering the illegal actions.