Amazon wants to get more into the food business, so naturally they were going to acquire somebody.  If somebody else offers more for Whole Foods, then Amazon will simply buy somebody else.

There are many items in food retailing that consumers WANT to go into a store and purchase in person.  They want to see it, they want it as fresh as possible.  You cannot accomplish that via online ordering.  Amazon realized that.

Plus, Amazon can use Whole Foods stores as a base for stocking and delivery of items that people are happy to purchase online.