Lost in the ear-splitting uproar over Whole Foods CEO John Mackey’s controversial venture into the health care debate, is a bigger, though less subtle story.

It’s a story about how a small, well-intentioned sustainable food company lost its way. It’s a story of how that company went from a single natural foods store in Austin, Texas to industry juggernaut, with every intention of dominating the natural foods retail category, in the nearly-identical way its conventional competitors came to dominate their sectors, i.e., achieving massive scale through acquisitions, new stores and eliminating smaller competitors.

Along the way, that company, Whole Foods, traded in any sense of purpose it had regarding regional food systems to pursue increasingly larger financial objectives, e.g., $12.0 billion in sales by 2010, up from $8.0 billion in FY08 sales and maintaining its 30% CAGR in sales since ’91 IPO. Today, Whole Foods, which publicly trades on the NASDAQ exchange (symbol: WFMI), owns the natural foods retail category, providing solid annual financial returns to its shareholders. Significant accomplishments considering Whole Foods’ humble beginnings.

But alongside this growth, a company with great potential to fundamentally change sustainable food lost its luster. Although shareholders, who have earned handsome returns over the years – 15% CAGR in stock price since IPO – cannot complain, sustainable food advocates can. Here’s why.

After acquiring 19 regional chains since 1991, beginning with New Orleans-based Whole Food Company and ending with its recent $565 million acquisition of Wild Oats (#2 national chain with 110 stores, compared to Whole Foods’ 191 stores), the resulting natural foods landscape now resembles the highly concentrated, conventional food retail space more than it does the regional food systems that sustainable food advocates identify as key to improving the food we eat.

The problem with Whole Foods isn’t necessarily its management or financial performance; it’s that the company has morphed into what amounts to a “sustainable” version of Wal-Mart and Kroger and every other multi-billion dollar supermarket chain. As evidence, the original Whole Foods Market opened in 1980 at 10,500 square feet, quite large compared to other natural foods stores at that time. By 2008, its 276 stores averaged 36,000 square feet, and it plans to open 70 new stores through fiscal year 2013 at an average size of 47,300 square feet, slightly above the conventional food supermarket median average of 46,755 square feet. Taken together, these stores will occupy over 13 million square feet of retail space, stocked with tens of thousands of packaged, processed and perishable items, purchased almost entirely through large national distributors, much like any other large supermarket.

There’s every indication that these massive Whole Foods “natural foods” stores will continue popping up in more regions, including smaller markets, e.g., Burlington, Vermont, a city of less than 40,000 citizens in a county barely breaking 150,000 people. Burlington is home to one of the more vibrant sustainable food communities in the country. There are no Whole Foods Markets or Trader Joes in this town. Instead, residents frequent food cooperatives, farmers markets and community supported agriculture (CSA) farms, purchasing above-average quantities of food from local farms and processors.