Just War Theory

The just war theory describes when Christians would kill others who seemed to be unchristian. Such as Martin Luther. Martin Luther wanted to kill many people who were against the religion of christianity or who were just simply not christian; such as the jewish. Martin Luther gave many persuasive speeches against others to kill, or just simply injure. The irony of this entire situation though is that Martin Luther (a christian himself) wanted to kill others. isn't it one of the commandments "thou shall not kill"? The fact that he himself had killed many causes him to be the face of an unchristian man. Isn't a christian who kills just like an individual having sex for their virginity?