I think you would be able to think more clearly about these topics if you made some additional distinctions among your hypothesis under consideration. Instead of "the Atkins diet is good", try "the Atkins diet allows me to maintain a lower body fat percentage than the SAD" and "the Atkins diet allows the typical person to maintain a lower body fat percentage than the SAD". Based on that study, you should decrease your degree of belief in both of these hypothesis, but to a much greater extent for the latter hypothesis relative to the former.
This seems like an authoritative 25-year research project that the Atkins diet is pretty bad:
http://www.nutritionj.com/content/11/1/40/abstract
Right now my belief is that the Atkins diet is good. It's backed by anecdotal evidence of trying a low-carb diet for 18 months following a 12-month low-fat diet and seemingly getting better results with the low-carb diet.
I'm counting on LWers to tell me how to update my belief in light of this study. Thanks.