Well, I hope you're right, but I think you're wrong. Here's why:
Amazon wants to dominate the world of retail, and Whole Foods currently targets a specific and smaller demographic than "The World". Amazon needs to expand the demographic to reach everyone else. The way they do that is by removing most of the expensive things Whole Foods carries, and replacing them with cheap, less ethical alternatives.
This means we'll eventually lose a lot of the things Whole Foods carries. For a lot of vegan and ethical suppliers, Whole Foods is the vast majority of their sales, and they'll just be shut down.
If their interest was in low quality, inexpensive supermarket locations, why wouldn't they purchase something like Publix, with its 1,154 stores, for a much cheaper price?
Furthermore, if you want guaranteed ethical, organic and fair trade goods, Whole Foods was always more about branding than reality on that front, anyways. Their stuff is better than most supermarket chains, but the independent stores still have them beat by a far margin.
If Amazon wants to target low end grocery retail, why do they acquire Whole Foods?
It makes business sense for them to let WFM stay high end, and start a Amazon Basics store to go down market.
Second, everyone I know who has ever worked at whole foods could talk for hours about their internal inefficiencies, food waste being a huge one. Their pricing was also almost whimsical, the most extreme example being their $4.99 "asparagus water".
My guess is that Amazon took one look at the books and saw that they could easily lower prices without suffering much in the way of profit loss. This doesn't necessarily imply there will be sweeping changes in quality.