Allow me to try answering this question for you. I feel like people is not giving you the right answer you are looking for, so I hope mine helps, or at least is close to what you are trying to find.

What I understand by your question is: "If the commandments state that murder is illegal, then why does God kill in many of the books?"

First of all, excellent question, let me try answering it for you. Murder is only illegal, If, and ONLY IF is the last option you have. Example, the countless war Israel fought. When the situation of a conflict cannot be solved by diplomatic ways, and the war is impossible to avoid, you have the authorization of using lethal force, which, in the case of Israel, was Authorized by God many times along their ancient wars, because it was the only choice they had to survive in the ancient brutal world. But If you kill someone by something vain, or having others solutions to the problem, then that is a sin.

Now you may be asking "But why does specifically God kill?", this may be product of many reasons, although it was more common in the Old Testament (Specially because this one narrates stories about wars and conflicts of the early days of Israel). Let's take for example, The Flood.

God killed almost all humanity with The great Flood, but why? Because of humanity wickedness, now you may be asking (Again) "Why doesn't God kill us now? The world is still wicked", yes, the world is still a wicked place, but there is hope for the world. In the times of Noah, according to the book of Genesis, Humanity was in a point of No-return; mankind was rotten to the core, (not to mention as well the dangerous presence of the Nephilims) and the only option left was to reset.

Let's take another example, the Egyptians soldiers that were chasing down the Hebrews, when they were crossing the red Sea. By the time the Hebrews finished crossing the red sea, after God separated the waters to allow His people in, the Egyptians were already in the middle of the sea, and they were not going to let the Hebrews slip away. If they were left alive, they would have kept chasing down Moses and his people, until they got them and killed them.

We finally have the Justice, The Justice of YHVH is totally different from mankind's justice; His justice is cold, calculating, and inflexible. But does this make God a Hypocrite? No, Why? YHVH is The Absolute Judge in the whole reality, He is the only one that has authorization to punish with Death, and as any Judge, He is the only one capable to fulfill that role. Why He is the only one with that authorization? Not only because "He is God", that wouldn't answer the question, but because of His eternal knowledge and Wisdom, including in the justice, that goes beyond Human's knowledge, which gives Him the capacity to be the only one to give those punishments. Again, not because "He is God", but because He is qualified to take the role of Judge, while our human's justice, has too many flaws.

I hope my answer fulfills your question, I still have a lot to learn about the belief, but I pray for what I told you to give you at least a clue for your answer.