Whole Foods is a business capitalizing on a market segment however they can. I buy a few select things at WF, and ignore the rest. Not everyone marries their personal beliefs with business income. In fact, most don't.
If I created a "Whole Foods" type store, I would be like a hawk to ensure that it stays my store only sold whole, healthy throughoutfood items. Imagine that! And while many peiople people have different ideas about what 'healthy' means, I would at least stick to a basis of what I think healthy means, based upon what I've learned, and what I would continue to learn on an ongoing basis.
The difference between that type of vision and Whole Foods is that the owner of WF knows very certainly that LOTS and LOTS of items sold in his store are very unhealthy for any human to consume. Therein lies the difference. Besides that, he is Vegan and pushes that agenda heavily, all while selling loads of unvegan foods (thankfully!). This is further confirmation that he is not concerned much with the underlying morale of trying to make the business model match up with any type of underlying morale he might have.
As Patrik says, let's call it what it is. It's a store that sells all kinds of foods, and only some of it is actually good for you by literally anyone's standards. If WF is guilty of "making people fat", I think it would fall under the premise that WF is guilty of tricking the gullible public by intentionally disguising itself as a health food store, while not remaining consistent with that model in its operations for profit.