Religion does not give people immunity so that they can kill others. NEVER is it okay to make someone suffer because of what you believe. Everyone is entitled to beliefs and opinions, and if your belief is that some individuals or groups should be harmed, you can think that. But if you start hurting someone (physically or emotionally), you are breaking laws.
It cannot be justifiable in the same way that it is not really justifiable that, if you are insane, you should be freed of your charges in court--you must still be punished for your actions. What you would plead if you were to suggest that your religion dictates you go out and kill people who do not believe, or you cannot persuade to believe, then you are pleading for insanity, a mental deficit. Christians should not go out killing atheists like myself because we choose not to believe, nor should Muslims engage in violent jihad (lesser jihad). If religion is meant as a unifying force, then violence is not truly the way to go about unifying people--it should be based on the persuasive argument you engage in with a potential convert, rather than by force. Violence due to religion is detrimental and results in purposeless death of many people, which is nothing that a functioning society should tolerate under the notion of freedom of religion.