Better translated, "Thou shalt not murder". Even God directs the complete decimation and annihilation of Israel's enemies in OT history, to such an extent that even after victory, the fields were to be salted and their livestock slaughtered and not eaten. See 1st Sam 15 in regards to the Amalekites.
There will be many killed who oppose Him and are killed in righteousness, while their being permitted to even live is considered immoral and unrighteous. Israel spent 40 years in the desert for far less a decisiveness in their warfare.
That may be so, but I believe that for Christians to draw the distinction between "kill" and "murder" is actually mincing words. Christ holds His followers to a higher standard than that, in Matt 5:21-22
Ye have heard that it was said of them of old time, Thou shalt not kill; and whosoever shall kill shall be in danger of the judgment:
But I say unto you, That whosoever is angry with his brother without a cause shall be in danger of the judgment: and whosoever shall say to his brother, Raca, shall be in danger of the council: but whosoever shall say, Thou fool, shall be in danger of hell fire.