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Whole Foods doesn't have a presence where I live (Victoria, BC, Canada), so I really haven't developed any opinions on the company. They do strongly remind me of Pilgrim Foods in John Brunner's novel The Sheep Look Up, though. The Guardian and Rolling Stone have both published an interview with the founder and CEO John Mackey which, I think, gives a great deal of insight into the company:

Contrary to what has been written about me I am not a "climate-change skeptic." Climate change is clearly occurring, and based on what I have read global temperatures have increased about 1.5 degrees Celsius over the past 150 years. We've been in a gradual warming trend since the ending of the "Little Ice Age" in about 1870, and climate change is perfectly natural and not necessarily bad. In general, most of humanity tends to flourish more when global temperatures are in a warming trend and I believe we will be able to successfully adapt to gradually rising temperatures. What I am opposed to is trying to stop virtually all economic progress because of the fear of climate change. I would hate to see billions of people condemned to remain in poverty because of climate-change fears.