When you take statements out of context, you can use them to prove anything. While I can't directly talk about the Koran (I've been meaning to read it), but I can about the Bible.

You cannot take statements out of the Old Testament without also including the New Testament books. The OT is about setting up history and pretext for what the NT teaches about life. Yes the OT has some very violent stories, but you cannot read through them and say "oh, this is telling ME, TODAY, to be violent". To do so is to say that killing intellectuals is OK today because the Khamer Rouge did it in Cambodia. Or that it's ok to drop a nuke on someone because we did it to Japan. The Old Testament is history and context so that you understand the importance of the coming of Jesus and his teachings in the New Testament, and no-where does Jesus's teaching tell people to take up arms and cause violence.