The Onion apologizes for calling 9-year old Quvenzhane Wallis a ****...

I can see why they'd apologize or why people would take it as harsh.

As for the comment about satire, it's not really satire it's absurd humor.

They do reversals and nonsense absurdism generally for the laughs. In reverse it would be like them publishing a piece on Hitler's misunderstood kindness to Jews. They would expect you to know it's absurd and meant as that kind of reversal. That, too, would draw outrage and apology, but it's really only people objecting because there's some sacred "too far" with pushing the humor/absurd. They shoot for those lines, but no one minds when they don't cross a big enough line.

Their piece that got picked up by Iran's news service as true was making fun of rural liberals having more values in common with Ahmenijad than Obama. Pretty insulting to the victims, but pretty funny too.