This article in Slate is a pretty good survey of potential problems with Whole Foods, most of which I've said (at least to myself) before. I don't buy organic produce when there is locally grown available, and I'm under no illusion that the organic produce arriving here from CA comes from small farmers. Do people really believe that small farmers have the marketing wherewithall to get a large conglomerate to ship their produce all across the country? Pfft.
It's an important point that the salaries and benefits for their employees are liveable. The article doesn't mention that the employees receive profit sharing, but I'm pretty certain they do, after a certain level of seniority.
I question the part about Whole Paycheck. I shop at Whole Foods now—it's right next door. Previous to that, I have shopped at Star Market and Stop N Shop. My grocery bill always seemed to be about the same. I'd like to see some evidence for the claim that WF is more expensive, because people always say it. I can think of some cases where it's true, like anything from the household or personal care section, but I'm thinking about just food here.