FWIW, the one thing I can agree with Sam Harris on is that European integration of muslims (and other minorities) is slow compared to the US because they have less of a commitment to freedom of speech. For all of our racial problems, the US does a better job of integrating immigrant communities because we have a culture of airing our dirty laundry, of hashing out our feelings - bigotry and all - and thus working through the differences rather than sheltering people from possibly being offended. Its ugly and frequently unpleasant but in the long run I think we reach a level of accommodation a lot sooner.
FWIW, I'm an atheist who married a woman from an immigrant muslim family although I've probably been in more mosques than she has.
The _low_ end is 15-20% who think honor killing is rarely/sometimes/often justified. The high end is 60-70%. How is this "fringe"?
So: do the teachings of those with a mantle of religion-X authority, on average, encourage or discourage honor killings? This is not a question we should avoid asking just because we want to be nice.
I don't see any evidence that Sam Harris has got this wrong.
Good point about being nice vs. reaching a permanent accommodation.
That said, he might just have an irrational us vs. them "liberals vs. racists" complex and be able to speak sensibly on other matters.