Because of this enormous ease of understanding the morality of an individual that you recognize - we can simply *define* morality as applying to only individuals. Hence hierarchies are by definition amoral - neither moral nor immoral.
Now remains the question whether hierarchies can behave as if they were moral :
There will inevitably be conflicts between morality of different individuals in the hierarchy. At such a time, does an individual follow the morality of his superiors, or his own? If his own, it is not a hierarchy any more. If of his superiors, the hierarchy is not behaving morally - it could be immoral or amoral but definitely not moral at this point.
Secondly, consider individuals performing duty when they will have to answer a superior but cannot ask the superior for instructions on the field because situation demands urgent response. His thought process is not only about legal and moral implications of his action - but also how it would appear to his superior whose morality he is partially aware of. So the aforementioned undue influence on an individual is not only of his superiors' morality , but also of his perception of their morality.
Thirdly, it is possible that under some circumstances, certain individuals' morality may not permit them to do some activities but they can more easily order others to do those same activities. In their own minds, they can blame the subordinates - or rationalize it away. Human beings, especially in moral department, are not rational animals - we are rationalizing animals.
So it is like an individual can playback sing for an individual actor - but a choir cannot. Due to the inevitable differences in frequencies and timings of members of the choir.