Ted's recent post is, I think, what I would have said after I finished ranting about Sam Harris. Violence is an intrinsic and un-ignorable part of human nature. It's why we love football, James Bond, and Halo. It's why it's a big deal that Appleton's violent crime rate is so low. Even people who are normally peaceful and pacifistic sometimes get the urge to punch people in the face. I know I do.
I think it's important not to deny this facet of human nature, especially when looking at the more violent passages of the Koran. I fully agree with Ted that acknowledging this side of human nature is not necessarily condoning it, and it's totally unfair to ignore all the millions of peaceful Muslims. And then there's the allegorical view of everything -- I know I didn't have trouble looking at those "awful violent quotes" and taking them metaphorically. In fact, it was really easy.
I suppose, ultimately, it comes down to what you consider good and bad. Is it good to believe that ignoring something bad will make it go away? Or is it good to face up to your inherent deficiencies? I believe the latter.