Thy shall not kill. Authority to kill comes from the CREATOR.

Thy shall not kill applies to those who have not be given the right to kill, and the authority to kill comes from the CREATOR alone. If you kill without the authority, you will definitely receive the punishment meant for those who break the thy shall not kill Commandment.
Those in the military (or those with the job of killing) have to be authorized by the CREATOR or law from the CREATOR that specify when a person is qualified to kill or qualified to be killed, so that the innocent or those that don't deserve to die are not killed. If you kill mistakenly then a qualified judge will determine what punishment is due for you. It's still a sin to kill in ignorance/mistakenly but the punishment isn't as severe as those who kill intentionally. There is the possibility of being forgiven by the CREATOR or HIS servant the Judge.
Do violence to no man