[ampaterry]

That translation of the commandment that simply states "Thou shalt not kill" is a bit briefer than it actually should be. Notice that the death penalty is prescribed for several offenses, which seems to show that the Bible contradicts itself - which it does not do.

In that commandment, the Hebrew word translated "kill" is רָצַח
which is pronounced "Ra-Tsach", and it is not simply kill as we usually use that word, but means to cause the death of someone who is undeserving of it. Most translations, even the New King James, use "murder" instead of kill. It forbids the taking of anothers life for personal gain, but does not prohibit capital punishment for a crime, nor lives taken in self defense or in defense of innocents.
It goes a bit beyond that, though - it also means that if through inaction you allow someone to die, you are guilty. If someone is starving and you have the means to give them food and prevent their death, yet fail to do so - you are guilty.

You absolutely have the right to defend with lethal force your life and the lives of others, both on a personal level and on a national level as in a war.
For my part, considering the usual result of a home invasion, if someone is kicking in my door I will assume they are goiing to kill me, and I will stop them with lethal force.