I think you've answered most of your own question. You pointed to self-defense and war as potential cases of acceptable killing. But the law in every country I know of allows for self-defense, and also allows for legislatures or rulers to declare war. We might add: for better or worse (worse , in my view) some countries allow for capital punishment. And so whether or not religion has anything to do with the historical origins of the law, there are very few nations, if any, in which killing is absolutely and always illegal.

Still, we do place a very high value on life -- perhaps even a "supreme" value, even if not an absolute one. But it's not at all clear that we have to use religious premises to end up with this view, and it's also not clear that there's anything irrational in thinking that killing is usually a very great wrong. One might think: if this is irrational, we need some sort of argument to see why.