If Amazon is smart, they will keep their brand out of Whole Foods, at least until they rehabilitate it some. Neither media or public sentiment towards Amazon is great right now for a variety of reasons, many of which have been posted on HN. Some people are getting disturbed that it seems like they can only get important goods from one company; indeed, this is basically the monopoly future that Amazon wants. Personally, I don't want to feel like I'm being stalked or "optimized" by Amazon at my local Whole Foods.
I don't think we've seen the end of non-Amazon retail yet. When almost every transaction is conducted through Skinnerian workflows developed by MBAs in Seattle and neural networks running in Virginia data centers, doing all your shopping at Walmart is an act of radical physicality.