Thou shalt not kill? Isn't this a little ironic given that the Hebrew Bible is full of killings?

Because that's the Israelite justification. What happened was that there was a religious/cultural war between the different Semitic tribes around the collapse of the Bronze Age and the Jews massacred their enemies, possibly to stop being massacred themselves, it's hard to know for sure. And then they told us after the event that god had instructed them to do it to, you know, make it seem more acceptable. It is pretty nasty, but it was a bad time to be alive. The Sea Peoples were raiding the Levantine coast, wiping out civilisations 1000s of years old, the regional trade routes [and food supplies] broke down and people were scared and fighting for their lives. You can't really judge them by today's standards.