I must say, Chomsky is one cantankerous son of a gun. Granted, Harris was less than flattering in his original treatment of Chomsky's points in The End of Faith (as he included near the beginning here), but in this exchange, Harris strikes me as a reasonable man. Chomsky, on the other hand, strikes me as a pedant used to an automatic deference from those he deigns to interact with.
While I agree that the tone of an argument has no ultimate bearing on its contents — they say not to shoot the messenger because of his message — I can't help but think about the power that tone has in an exchange. If men were perfectly rational beings free of the frailties and cognitive biases inherent to human psychology, then the tone one takes would make no difference because we'd be able to weigh the argument without feeling personally attacked, our flight or fight response kicking in and shutting down the higher-functioning parts of our brain, or as Spock would say, becoming emotionally compromised. Harris, it seems to me, took the pain to create an environment relatively free of hostility, adopted a tone that engendered a safe channel of communication. Chomsky got irate to the point of being emotionally compromised anyway. Because that's what this is about right? Sam Harris published this because he wanted to show how incapable Noam Chomsky is of a clear-headed debate. I think, in that sense, he's right.