The Mother Earth-friendly crowd might enjoy the natural, organic foods lining the pristine shelves of their neighborhood Whole Foods Market (WFMI), but some of them don’t seem as appreciative of the politics of the company’s chief executive.

John Mackey, the controversial co-founder and CEO of Whole Foods, penned an editorial last week in The Wall Street Journal, in which he came down hard on Obama’s health care reform plan. Mackey called for a move toward “less government control and more individual empowerment” rather than “a massive new health-care entitlement that will create hundreds of billions of dollars of new unfunded deficits and move us much closer to a government takeover of our health-care system.”

Unsurprisingly, not all of Mackey’s Prius (TM)-driving customers appear to agree with his views. (Though he's certainly managed to alienate them before: see CEOs Gone Wild: John Mackey for more.) Now, some of these once loyal patrons are threatening to boycott Whole Foods to demonstrate their opposition.

Those Whole Foods shoppers with a left-leaning political bias and a web connection have moved to the Internet, where they’re using social networking sites like Twitter and Facebook to press for the boycott.

Of course, boycotts are difficult to orchestrate and research analysts covering Whole Foods don’t see the threats as posing any kind of real cause for concern for the company. Frankly, it’s hard to see how these shoppers could really act on their political impulses: if they steer clear of Whole Foods altogether, where else can they go to buy all that organic applesauce?

This morning, longtime market pro Dennis Gartman weighed in with his views on the controversy: “People who will go to a store wearing Birkenstocks and socks will take almost any outlandish position, and they’ve taken a position opposed to Mr. Mackey’s editorial in The Wall Street Journal last week that took Obamacare to task,” Gartman wrote. “When your own supporters are willing to abandon you, who will support you? It seems like a good question.”

But enough about whether or not you should shop at Whole Foods. The bigger question is whether or not you should dump the stock.

S&P equity analyst Joseph Agnese thinks you should avoid Whole Foods like a carton of spoiled milk. Agnese, who currently has a “Sell” rating on the company, says the food retailer is now just looking too pricey, says the analyst.

“It is a great company but the valuation isn’t matching what the growth will be,” Agnese tells Minyanville.

Indeed, Whole Foods shares have surged 190% in the past 6 months, and it now looks expensive relative to its expected earnings power, with a price/earnings to growth ratio of 2.13. (Anything under one is considered a good deal.)

Looking ahead, Agnese sees problems for the company, as spendthrift consumers coming out of this recession save more and spend less, which will keep a lid on the sales growth at Whole Foods, he argues. In the third quarter, the food retailer said sales edged up 2% while sales at stores open at least a year slipped 2.5%.

“People aren’t trading up like they used to and they will be slow to return to that type of behavior,” the analyst says.

Where's the stock headed from here? Katie Stockton, chief market technician at MKM Partners, says Whole Foods is poised to fill its gap down to $24.87, at a minimum, as the market pulls back.

For those stock pickers that are still interested in playing with the grocers in general, Agnese does offer some suggestions. Broadly speaking, he likes those retailers targeting cheapskate shoppers such as Kroger (KR), which he rates a “Buy,” with a price target of $25.

“Those who differentiate to the higher end aren’t as well positioned as those who cater to more price-sensitive customers,” says the analyst.