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. "When we destroy a population," Allah says, "then we destroy them utterly" (17:16-17). Such words are as unamenable to rationalist disambiguation as the order to "fight those who do not profess the true faith till they pay the jiziya (poll tax) with the hand of humility."
Second, Islamic debate underestimates the weight of Muhammad's personal legacy. The problem of Islam lies to a significant extent in the claim of its prophet that his words and acts provide the universally valid standard. The Hadith--Muhammad's words and deeds, as supposedly recorded by his contemporaries, which must be obeyed by every true Muslim--contain huge stumbling blocks for a would-be Aquinas or, say, Hardball guest, Irshad Manji (author, "The Trouble With Islam Today"), in Cairo. The Koran is to be recited, the prophet of Islam declares, not subjected to analytical study by a reasoning mind: "Whoever so interprets the Quran according to his opinion, let him seek his abode in the fire."
Third, Muhammad invented jihad in his lifetime; Islam was spread by jihad in its first century, and it has been defined by jihad ever since. Islam had developed a doctrine, legal system, and historical practice of mandatory violence against nonbelievers many decades before the Mu'tazilite thinkers (believed Allah was accessible to rational thought and inquiry) were born. Muhammad's early followers adopted bloodshed and terrorism as a divinely ordained method. The Jews of the Old Testament exterminated non-Jews in the name of their God, but they did so on specific commandment against specified enemies. To the Muslim warriors, the command was open-ended for the outset.
Attempts to "reform" Islam has been tried before. Those who attempt to unveil a more rational variety of the Islamic faith are seen as belonging to Islam as much as Voltaire belongs to Christianity. A redirected Islam of a reform nature would no longer be Islam. For the majority of Muslims, any such attempt is considered as heretical today as it was at its foundation.