Once he can show that the simple version can be questioned, he opens room for further questioning.If you want to call the simple version of a theory into question, present the simple version of the theory. Don't obscure 90% of it. Taubes doesn't present the version I described because the version I described is pretty hard to question. Has Taubes shown us that we need to question the theory that 7.5 extra strips of bacon each day will make you fat?
Also, no one believes that traditional calorie counting is perfect. It's a good first approximation, but there are corrections to be made. You've identified one - you can't absorb 7200 calories in a single day. But then again, I never heard anyone in the nutritional mainstream claim that Thanksgiving dinner is what is making America fat. They just make claims like, for example, 7.5 strips of bacon/day might make you fat, and 7.0 strips of bacon will keep you fat but not make you fatter. (Substitute cookies for bacon if you want.) There are others, many of which are already well known. Pick up any sports medicine book to learn all about them.
As for "designing a solution to obesity", we already have the solution for the vast majority of people: eat less and exercise more. Taubes is trying to sell books by misleading people about the theory underlying that solution (i.e., ignoring 90% of it). It's hard to see how that is helping us get to a better solution than what we have now.
And I don't think that his portrayal of conventional wisdom is that far off: we have entire industries based on shaving off a few calories from our desserts, and many people seem to believe that if the fat slobs would just park at the far end of the parking lot and walk another 100 feet they wouldn't be fat.
You seem to be confusing mainstream nutrition science with people hawking their own wares. Modern medical science, in the form of an about.com calculator, says that you burn about 2 calories by walking 100 feet.
http://walking.about.com/library/cal/uccalc1.htm
It might not be exactly right - maybe it's 1.5, maybe it's 2.5. But it's a good first approximation, and so is calorie counting.