Question

Good evening,
The whole world, myself included, stands shocked by the bloodlust and barbarity of the ISIS organization, which makes no distinction between children, women, and innocent people, and whose results we saw just this week in the attack in Britain. 
I assume this is a well-known question that has already been asked, but even so I won’t refrain from asking: why is our commandment to wipe out Amalek—women, children, and the elderly—different from them? After all, they too claim that they are doing it in the name of God; from their perspective as well, we are sinners, and our destruction in their eyes is a commandment of Allah for which they will receive “reward.”
Where is our morality in all this? And perhaps we too would be considered super-terrorists if we went and destroyed an entire people in the name of God.
I would be happy to hear your opinion.
Thank you.