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***there were times when God told them to completely destroy their neighbors because their sins had become so gross that they would bring down the spiritual sensitivities of Jews.***

John 18:36
Jesus answered, My kingdom is not of this world: if my kingdom were of this world, then would my servants fight, that I should not be delivered to the Jews: but now is my kingdom not from hence.

If a man in self-defense uses more than necessary violence, it will be unlawful: whereas if he repels force with moderation, his defense will be lawful.... Nor is it necessary for salvation that a man omit the act of moderate self-defense to avoid killing the other man, since one is bound to take more care of one's own life than of another's. [St. Thomas Aquinas, STh II-II, 64, 7, corp. art]

To be sure, St Thomas also states that the intentional killing of the innocent or undue violence is a grave sin but violence in protection of ones self or another to the point of killing is does not prevent salvation.

I agree with St Thomas.