The Sixth Commandment’s “Thou Shall Not Kill” is obviously not absolute, for within the context of the rest of the Bible, it can be seen that God allows for self-defense. Also, the Bible establishes the right of the state to administer capital punishment. And then there is the matter of the Lord leading armies to war. The commandment, then, isn’t saying don’t kill under any circumstances. It is saying don’t take a life without proper justification.
I believe God holds Himself to the same standard, but more magnified. Like an earthly judge, He has facts before Him to consider. Unlike an earthly judge, He brings to bear on those facts, infinite knowledge and wisdom. That would include knowing the harm that some would cause against His plan of salvation if allowed to live.
That God should have the right to kill should not be a strange thing. After all, we acknowledge and cede the point that earthly judges have that right. We understand and grant them that power over life because of their knowledge, training, and wisdom.
Much more is God capable and within His right to administer His own law.
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A related post from a different angle is God Killing People – Just or Unjust? Click here to read it.