Three primary points are usually left out of the Islamic discussion. The central problem with most Islamic analysis is that it underestimates the weight of the moral and intellectual chains imposed on Islam by its founder and his early followers.
First, the most irrational, violent, and intolerant chapters in the Koran--the "Verse of the Sword" (Sura 9:5), most notably--were "revealed" in Medina, late in Muhammad's life, after the ones potentially amenable, and therefore they abrogate the earlier chapters. Allah's order to "kill the unbelievers wherever you find them" is an injunction, not a suggestion.
