A huge topic and lots of pre-suppositions and assumptions are made in these kinds of discussions. Also, not having formal theological training, my response is more limited.

First of all, in reality, anything the God of Heaven, our Creator, sustainer and governor of His universe does is not up to the subjective character evaluation of His creatures. He isn't to be compared with false religions imagined by some of His rebellious, fallen creatures. If we don't start with that, the discussion cannot be congruent.

If man's intellect is the center of all things, such an evaluation cannot be congruent.

The starting point really is the sovereignty of God (versus the sovereignty of man).

If man's mind is at the center, God will be judged "unfair" by lesser evaluation of man's ego. (This is why the "five points" or "doctrines of grace" are a wise point to draw out, explain, debate, and discuss with both believers and nonbelievers alike. God really likes it when we "get it" that we are not really the center and measure of all things. That's where Christian growth really begins).

The sixth commandment, "do not kill" is in words that are more carefully understood as "thou shalt not murder." Nations engaging in war are obviously not in view here (otherwise God would not have commanded Israel into battle so many times).

Self defense is a biblical concept that we could draw out here. In no sense (despite the wicked imaginations of the killers, liars, God mockers who planned 9/11) was their attack self defense. A good case can be made it was not even in accord with their own religion.

In the end, there is something that we, as fallen, self-centered human beings do not want to accept. It is very understandable in light of what God has revealed to us about our nature, through Scripture. We do not believe has a right to do with us, as His created beings as He sees fit. That bothers us...

Whether it is God Almighty's right to reserve a sabbath day unto himself for us to worship,

Reserve a portion of our material income to give back to Him as offerings,

Or His right to give or take life as He alone pleases.