This is actually an important and interesting conversation to have. Indeed, Greenwald almost exclusively deals in important and interesting conversations, and that's to his credit. But this article is basically a plea to readers "don't associate me at all with the dumb arguments of people on my side, but make sure you hold Sam Harris responsible for everything anyone I disagree with says".
I can see how Greenwald achieves such success as a columnist and as a lawyer. He argues his positions with great passion and conviction, and it does a great job papering over how flimsy they are in a lot of cases.
On the Harris thing: we've gone over these things enough on here to know that I disagree with him on the torture (although he's not an unqualified supporter) and on Iraq, but agree on the war on terror, etc. On the question of Islam (the subject of this article), I think it's entirely appropriate to say that modern Islam - not all of modern Islam, but considering all the elements and not just picking the "good" ones - is indeed uniquely threatening to liberal civilization and insofar as it imposes itself on innocent Muslims and non-Muslims, it needs to be met appropriately (which, under some circumstances, also means lethally). I am very much in favor of the distinction between "Muslims" and "Islamists" precisely because modern Islam is diverse and not uniformly problematic. But I don't think it's inappropriate at all to note that Islam's "Islamist" faction is more prominent and more dangerous than say Christianity's "Christianist" faction. Five hundred or a thousand years ago you could probably say the reverse. At that time liberal elements dissented (with mixed results), left Europe, or (eventually) reformed the problem. But today, it is the Islamist community within the wider population of Muslims that poses the real threat to liberal civilization. And you know what? You can say that without supporting U.S. policy (I support some parts, but not others)