The saddest thing I can say about this story is that it doesn't surprise me at this point. The fact that the editor in question is Native American rather than white is a slight twist, but doesn't really change anything. In fact, his prejudice or lack thereof is not really the issue. September 11th made racism cool again, and science fiction was dismayingly susceptible to the bug.
This blogger posts a response, and is immediately confronted with a commenter who conflates Islam with jihadism. The latter is a somewhat nonsensical word to begin with--talk about "fightism", "crusadism", or "strugglism" and watch the kinds of looks you get--but some word may be needed to describe the ideology of actual terrorists. Thing is, when you ascribe such an ideology to the vast part of the Muslim population, that makes things scarier. It also makes things easier, too much so. Again, not a surprise. I could link to some essays by Dan Simmons, but it's getting late and they're not the entertaining kind of creepy.
And no, it doesn't end with one outgroup. You thought it would? Note that Larry Niven suggests scamming Hispanics out of seeking medical treatment, and he gets high-fived for being "politically incorrect."
My sense is that this kind of attitude is more prevalent in speculative fiction than it was twenty or forty years ago. Maybe I'm wrong, but it's kind of a depressing sight.