The New Yorker refused to run his bin Laden story? The My Lai story was published in the St. Louis Dispatch, only 30 papers picked it up initially. Only the Washington Post published about Watergate for months (with a few exceptions). Abu Ghraib was barely reported until the pictures came out. That the commissar at the New Yorker would not affix his signature means little to me.
The official story was, and in your mind presumably still is (though it seems to be in tatters now) that Osama bin Laden sat in a compound in Abbotabad, to the complete ignorance of all high Pakistani officials, including those living less than a mile away at the Pakistan Military Academy. Tariq Ali called this risible in the days after the raid, as did some of the Pakistani press. It's a completely ludicrous story. Later investigation by Pakistani journalists, Hersh and others uncovered even more. The official story was known to be ridiculous when it was announced. You are correct that he was pummeled for publishing the story and about the New Yorker though. I am not sure what has been refuted, other than the US government sticking by its original story. I guess it all comes down to whether one believes IF Stone's old journalistic maxim "Governments lie". People seem more interested in ad hominem attacks on Hersh, appeals to authority etc. as opposed to looking into whether the bin Laden raid story was true. Because the idea that no one in high position with connections to the Pakistani Military Academy had no notion bin Laden was there is laughable.