It's quite a weighty subject when you think about it, and i'd applaud the writers for broaching it. It was never really that didactic, or came at the expense of plot.
It all seemed to me to be a comment on the treatment of prisoners, and how that treatment of prisoners of war can give a reflection of the morality within a society. There is a duty of care involved.
In killing (or torturing) the prisoner, it was not only boneheaded due to the hostage being their only bargaining tool; but she also relinquished the moral legitimacy of the human race who she was said to represent. It doesn't matter what the morality of the HomoReptilia was, because the Doctor was asking her to aspire to a ideal sense of morality, not a relative sense.
You can empathise with the situation she was in, but killing the prisoner, it was both practically dumb, and morally very wrong. Hence the Doctor would see this behaviour to be the worst aspects of humanity.