In English law we have the offence of gross negligence manslaughter, where death is the result of a grossly negligent (though otherwise lawful) act or omission on the part of the defendant. In most US states the term would be Involuntary manslaughter. In other words, we are held responsible for the unintentionally evil consequences of our actions when any reasonable person would see that the action in question could well have such consequences.
Surely the same rule should apply to scriptures? Even if the Bible or Quran did not explicitly encourage violence, their language should not be such as to provide an excuse for it. If a group of people commit enormities in the name of a religion and they can site texts which appear to justify this, then surely the religion should be held responsible. To say that the extremists are not true members of their faith is no more than the "true scotsman" fallacy.