I don't know when the "thou shalt not kill" ever applied, especially since there are plenty of times in the OT when the Israelites killed their enemies, and God killed plenty of people. Maybe it only applies to other members of your church, like when I had a fundie tell me that Jesus' command to "love your brother as yourself" only applied to "other brothers in Christ" and apparently it was OK to be a total dick to non-Christians.
Christian apologetics is the art of rolling a dog turd in sugar and selling it as a donut.