While the vast majority of Muslims aren't extremists, a more important distinction must start being made -- the distinction between moderate Muslims and reform-minded ones.
Moderate Muslims denounce violence in the name of Islam but deny that Islam has anything to do with it. By their denial, moderates abandon the ground of theological interpretation to those with malignant intentions -- effectively telling would-be terrorists that they can get away with abuses of power because mainstream Muslims won't challenge the fanatics with bold, competing interpretations. To do so would be admit that religion is a factor. Moderate Muslims can't go there.
Reform-minded Muslims say it's time to admit that Islam's scripture and history are being exploited. They argue for re-interpretation precisely to put the would-be terrorists on notice that their monopoly is over. Re-interpreting doesn't mean re-writing. It means re-thinking words and practices that already exist -- removing them from a seventh-century tribal time warp and introducing them to a twenty first-century pluralistic context.
I think this is in general quite right, although as usual Manji tends to assume that all reform-minded Muslims will have views more or less like her own, when I think it's pretty clear that most reform-minded Muslims will have views much closer to those of the moderates than to Manji's. I think it is also a little too quick to assume that moderates in general are abandoning the ground of theological interpretation to extremists. We shouldn't underestimate the slow pressure of the quiet millions. The problem with moderation as opposed to reform is speed, since moving slowly is a problem when injustices are involved, as they are here. When something needs to be torn down, reform rather than moderation is needed; the strength of moderation is in building something sure and durable over long decades and centuries, not in changing the things that need to be changed now.