A lot of resources were put into the story, apparently - it's an attempt to look at the process whereby a kid who looks like that, who does not conform to the usual wailing stereotypes, nonetheless became a terrorist. Assuming the article demonstrates what they claim it demonstrates (I have not read it yet, but intend to pick it up today *because* of the controversy - I wouldn't have cared before, but now I want to read it), then the shot they chose, which has previously run in other publications including the NYT, was the right shot to use.
But most of the internet seems more concerned with excising the killer from the ranks of humanity by effigy, and RS here has refused to follow that script; I think the idea that it will sell more issues is a dubious one, given the current tone, and I honestly don't believe they expected this. They thought they were publishing in America, after all, with that whole first amendment thing - this is the internet.
As a side note, it's nice to seemingly have found a place where people understand the first amendment. And I say that as a Canadian. :>