Faith as Knowledge

I've been reading The End of Faith by Sam Harris, which is on the face of it an argument that certain types of so-called knowledge, mainly religious faith, are not only misleading but ought not be tolerated because of the danger that those who believe may put everybody in. Harris is more than heavy-handed, and his arguments are steeped with question begging. Further, while he gives serious nods to the history of what I might term 'religious-inspired violonce' in a chapter that discusses the Crusades and the Jewish Holocaust (both of which he counts as religious and political), for a good chunk of the book (though I'm not finished with it yet) he focuses on Islam in particular, quoting the Koran (ad nauseum, actually) and other texts important to that religious tradition and basically saying one simply can't be a Muslim and not want to kill people who aren't Muslims. He clearly doesn't back up these sorts of claims in any meaningful way--it reminds me of when I was 19 and I would argue with Christians that they just couldn't be christians if they weren't following Deuteronomy and stoning people left and right.

Still, one of his main points does have a certain ring of truth to it for me: Are there certain ways of believing or knowing which we should always condemn? Should appeals to faith--and a subsequent definition of faith as something like 'knowledge that can't be wrong' or 'knowledge that doesn't ever need, even in principle, to be justified--be struck down as just not good ways to believe?

Big can o' worms, I know, but the whole quest for certainty-through-faith does seem to take on some dangerous consequences for all.

Thoughts?