The commandment is actually "you shall not murder". There's a distinct difference between killing and murdering; murder can be categorised as only a small subset of killing. I could be misled but I'm under the impression that to old testament era Jews killing a non-jew was never murder.
2 This is what the Lord Almighty says: ‘I will punish the Amalekites for what they did to Israel when they waylaid them as they came up from Egypt. 3 Now go, attack the Amalekites and totally destroy all that belongs to them. Do not spare them; put to death men and women, children and infants, cattle and sheep, camels and donkeys.’
The Torah states Goyim (non-jews) are the same as beasts, but not necessarily as high on the ladder as livestock. The discussions in the Torah entertain all sorts of unsavory positions (inb4 muh context), but the gist is there is no serious punishment for lying to, stealing from, injuring, maiming, killing or raping Goyim.
Their holy books are cram-packed full of fucked up shit, but the hatred and active frustration of the Goyim is an overarching theme.