However, I am quite aware the Koran teaches war against infidels in various parts of its ever poetical ramblings. However, the Good Book teaches no such thing. So, the question is "Who was/is really following their religion and who was/is perverting it?". Answer that question and you have an answer to your problem with the Inquistions, etal.
Jesus addressed this a few years back when He said, "Not everyone who says to me, 'Lord, Lord', will enter the kingdom of heave, but only he who does the will of my Father in heaven...then I will tell them plainly, 'I never knew you. Away from me, you evildoers!"