I am not sure how you can read accusation of religiously motivated blindness/idolatry as anything but an attack really, it isn't a well-reasoned argument against a position, just ad-hominem.
Coincidently I am currently reading the aforementioned book myself (oh no, I am a religous loon!!), and if anything I get the impression of an exacerbated person basically pointing out that:
1: The current status quo in nutritional science was established before there was large scale data to confirm/refute it. It was heavily influenced by very few (I believe he mentions 1 or 2) specific scientists and became orthodoxy almost through force of will not necessarily because the data (which they didn't have) actually supported the hypothesis.
2: There are now numerous studies and quite a bit of data that seem to at least point to alternative hypothesis that should be explored. I don't recall yet having seen the author claim even the carbohydrate hypothesis he talks about is correct, just that it should be getting more study/attention than it is in main-stream nutritional science, and that it is better supported by the study data we do have than the currently accepted hypothesis which the studies we undertaken to test.
3: The idea that sedentary lifestyles coupled with abundantly available food just doesn’t track with the actual data as obesity seems to track much more closely with availability highly refined carbohydrates and massively increased sugar consumption. That said both could well play into it, it isn’t necessarily an either-or but much like the famous global warming vs. number of pirates graph it also doesn’t show causation, just correlation, and perhaps meaningless/misleading correlation at that.
4: Explaining obesity by overeating is as useful as explaining alcoholism by overdrinking (okay, I just threw that in because it is a funny quote :))
His primary push that I have taken away thus far is ‘we should be exploring this hypothesis, which isn’t actually terribly new nor is it terribly radical’. He claims people generally aren’t for unclear reasons (though I haven't picked up any sort of conspiracy vibes yet, which I was expecting). I have looked around for someone to refute his book but all I found was a weak refutation in Reason[1] which he responded to, and in my opinion, destroyed the critique quite handily [2]. I would be very interested in any responses that actually take to task the quoted studies / science from his book instead of attacking him by-proxy by calling Atkins a kook.
[1] http://reason.com/archives/2003/03/01/big-fat-fake/print
[2] http://reason.com/archives/2003/03/01/an-exercise-in-vitriol...