Chomsky has spent most of his life debating so his aggressiveness in this case seems to stem from how other people view the discourse (or how he agrees or disagrees with Sam) initially.
I would put that to an 87 year old academic who's vast library jammed in his head makes discourse with Sam (who I've listened to his podcast and doesn't typically source arguments and occasionally comes across as an ideologue) a little frustrating. Or maybe he's just old and crotchety.
"Comes across as..." is, of course, subjective; to my eye, Chomsky comes across as justifiably skeptical at the outset, and reasonably irritated as the exchange continues. Doesn't, to me, seem anything like "rabid" (much less "overly rabid" -- a description that is quite odd, as it seems to suggest that there is an appropriate degree of "rabid"; when you've chosen "rabid" as your metaphor, you've kind of ruled out "overly" being a useful modifier.)
Thanks for posting this, just read the whole exchange. Wow, Chomsky is certainly in an entirely different league here. I don't think Harris even understood what Chomsky was trying to emphasize.
http://www.samharris.org/blog/item/the-limits-of-discourse