well,
A - im a jew. living in israel. fully fluent in hebrew and english
B - im a practicing aetheist
C - i have some knowledge of the Torah, the New Testament, some buddhist writing, etc (due to my interest in religions)
MY view is that the commandment translates as
Thou shall not MURDER
i believe it means the generic - dont be bad, killing people for fun or whatever.
THERE are however LOTS of exemptions to this.
a favorite of mine is "do onto them before they do it onto you" (translation of spirit of verse)
also, IIRC, joshua went around clearing the lands of nonjews while establishing the hold of jews in the holy-land.
jewdaism is a peaceloving religion, that sanctifies life, and FORBIDS TAKING ANY LIFE (human. food is still food

) UNLESS you are threatened wih death yourself.
IN ORDER to save lives you may, and SHOULD take life.
self-defense is NOT MURDER and as such doesnot violate said commandment.