"...it sets up a health amount of skepticism towards the idea that our innate cravings are in fact harmful."
It's modern processed food that's harmful.
We evolved to cope with the amount of salt, sugar, carbohydrates etc. that was readily available to our ancestors on a hunter-gatherer diet (we would've reached an evolutionary dead end otherwise if our "innate cravings" were not useful to us in a survival sense) - you would have to do a lot of hunting and gathering to get the amount of salt, sugar, saturated fat etc that a single fast food meal provides - it was relatively rarer so we have cravings to ensure we got enough of them back when they were scarce.
Evolution is a very slow process. Adding syrup to carbonated water, advertising the crap out of it and selling it at huge markup (coca-cola) can happen over the course of a single human's lifespan.