If there is one restaurant that has increasingly garnered favor with the vegetarian and animal advocacy crowds in recent years, it is undoubtedly the fast-growing, fast-casual Chipotle Mexican Grill.

The evidence is unambiguous: Chipotle won People for the Ethical Treatment of Animals’ (PETA) Peta2 Libby Award for Best Vegan-Friendly Restaurant Chain in both 2011 and 2012. Last year, the restaurant’s new sofritas – shredded, braised, spiced tofu – made three of VegNews Magazine’s top 15 vegan news stories, and took home PETA’s Best New Vegan Food Item award. (That product has just launched nationwide.) Chipotle also ditched the bacon in -- and thereby veganized -- its pinto beans. The chain has even garnered praise from the Humane Society of the United States.

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This is no accident. Chipotle has hardly been shy about promoting its vegan options or professing its commitment to animal welfare. The company has put up billboards proclaiming that it is “Pro-Chicken,” and that its animals have been “Raised with Care.” It also produced two animated shorts decrying the horrors of factory farming: “Back to the Start” and the much-buzzed-about “The Scarecrow,” which also spawned a companion iPhone game.

Just last month, Chipotle premiered an original Hulu series, “Farmed and Dangerous,” in which a young, bright-eyed, farmer-activist “committed to better farming practices” takes on the PR machine behind evil, industrial “Animoil.” The four episodes of “Farmed and Dangerous” cost Chipotle about $1 million, which may indeed prove to be money well-spent, as Chipotle’s explosive growth has been attributed to the story the company tells about how its food differs from other fast food. Between 2007 and 2013, Chipotle more than tripled the amount of “natural” and “responsibly” raised meat it served, to over 130 million pounds.

This is all part of Chipotle’s commitment to serving what it calls “food with integrity,” which includes “treat[ing] animals with dignity and respect” and “allow[ing] them to display their natural tendencies.” Founder and co-CEO Steve Ells has explicitly promised to run his business “in a way that doesn’t exploit animals.”

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So why are animal rights activists protesting against Chipotle?

The protests began last March when a small group of Bay Area activists with Direct Action Everywhere (DxE) disrupted two Chipotle restaurants in Oakland and Berkeley. The activists stood in line like regular customers, but when they approached the counter, they unfurled a banner that took direct aim at Chipotle’s rhetoric: “Responsibly Raised? Unconditionally Loved? Brutally Murdered,” it read.

After activists in six cities staged “die-ins” at Chipotle restaurants in October, the protests started gaining momentum. By November, they had spread to 11 cities in the U.S. and Canada and by December to 16 cities. Now, the initially sporadic protests have developed into a campaign against Chipotle with the tag line, “It’s not food. It’s violence.” DxE, which I have advised on communications matters, holds protests against Chipotle at least once a month.

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I asked Wayne Hsiung, one of DxE’s organizers and a personal friend, about the rationale behind protesting a company that appears to be at least nominally attending to animal advocates’ concerns. “When you look under the ethical veneer, there are few (if any) companies worse than Chipotle,” Hsiung said. “Sure, it offers a vegan burrito. Yes, it pays lip service to animal welfare. But it is one of the fastest growing animal killers in the world. It spends millions of dollars every year on ‘humane washing’—deceiving the public with fraudulent claims of ‘respectful’ conditions. But killing is inherently a violent, not humane, act.”

Chipotle has come under fire before — for example, when it reverted to factory-farmed meat when the supply of “responsibly raised” meat has run short. And even industry publications have joined in outing Chipotle for sourcing from the West Coast’s largest ranch. The company has been shown overstating its claims and marketing itself with terms, like “natural,” which have no actual regulatory meaning. In short, Chipotle has been criticized for failing to live up to its own hyperbole.

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None of this, however, gets to the heart of DxE’s complaint. The group is not protesting Chipotle for having fallen short of its "humane" claims. They are taking issue with those claims themselves.

“There is no such thing as ‘humane slaughter,’” DxE says on its website, “and yet mainstream discussion of animal abuse is dominated by questions of ‘care’ rather than ‘killing.’ We need to shift this debate away from bigger cages and better deaths, and back to the central issue: whether we should be killing animals at all.” In short, DxE is not saying that Chipotle is misleading the public by falsely claiming to “[do] things the right way.” They are saying there is no right way to do the wrong thing.

The protests are certainly thought provoking. Ever since the food-culture zeitgeist swung strongly against factory farming, “humane” treatment has become the presumed alternative to an undeniably brutal system. But DxE’s protests raise the question of whether, in the frenzy to market and consume more humane animal products, we are completely ignoring the fundamental moral issue. Why, for example, is cutting off chickens’ beaks unacceptable cruelty, but cutting their throats is perfectly fine?

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Even if we put aside the hardly trivial matter that many standard industry practices -- such as un-anesthetized mutilations and intensive confinement --are routine in “humane” animal agriculture, as well as the fact that large-scale production requires efficient mass killing. The most unadorned slaughter is still hard to stomach — Chickens writhing and shrieking (Warning: graphic video) after having their throats slit; terrified cows struggling to escape the chute that leads to death; and pigs that are “as happy as happiness” unsuspectingly hauled off to a slaughter plant.

Indeed, an interesting paradox arises as we increasingly recognize that meat, dairy, and eggs come from individual animals with interests, emotions, and the ability to form relationships. There is something deeply disturbing about an animal coming to trust and feel safe in someone’s care, only to be betrayed in the most profound way by that same person—less brutal (maybe) than industrialized production, but equally wrong. But this is the best that can ever come from something as Orwellian as “humane slaughter.”

Pasture-based pig farmer Bob Comis has written movingly about being “haunted by the ghosts of nearly 2,000 happy pigs” that he has transformed into “happy meat,” and the “final crisis of conscience” that drove him, just a few weeks ago, to become a vegetarian and start winding down his life as a pig farmer. (Comis has also demystified many of the terms tossed around by companies hawking their wares as more humane; explaining, for example, that pigs raised in “deeply bedded pens,” like an unknown number of Chipotle’s, are most often raised “intensively” in what are “essentially humane CAFOs”—that is, factory farms.)

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DxE hopes to similarly haunt a company that is recasting its meat and dairy products as, in the words of Elizabeth Weiss in The New Yorker, “not only tasty, [but also] virtuous.” It is a curious kind of virtue in which “happier, healthier lives” for the animals is good not only because the animals live better, but because such treatment also produces “the best pork we’ve ever tasted.”

Indeed, sales of Chipotle’s carnitas doubled, notwithstanding a price increase, when the restaurant switched to “all-natural” pork.

Can a corporation that serves millions upon millions of pounds of meat and dairy -- and keeps selling more and more -- avoid exploiting animals? After all, the upshot of Chipotle’s masterful marketing has been explosive growth: A 1000 percent increase in market capitalization over the past 5 years. The company opened 185 stores last year, and it plans to add nearly 200 more in 2014. Co-CEO Monty Moran says “there’s room for thousands more.”

In the last Quarter of 2013, each of Chipotle’s nearly 1600 stores brought in an average of $622 more per day, compared to the same period in 2012. According to Bloomberg Businessweek, this last quarter's growth amounts to about 80 more burritos per store per day. Unless all these additional burritos are filled with beans and sofritas -- the latter of which currently account for a mere 3 percent of sales in the 40 percent of Chipotle restaurants where they have been introduced -- and left off the cheese and sour cream, the number of animals slaughtered and exploited by Chipotle is increasing.

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All of this makes Chipotle a pretty formidable opponent for a small group of grassroots activists, even if their numbers, too, are growing. But Hsiung says DxE is undaunted by the David-vs.-Goliath odds and that the group’s goals are not economic, but cultural. “Triggering a much-needed dialogue on the status of non-human animals, not costing Chipotle a few dollars and cents, is our primary campaign objective,” he told me.

What these activists are doing isn’t targeting Chipotle so much as using it as an arena in which to start a public debate about the morality of eating animals. From all appearances, Chipotle’s marketing seems to have created the ideal stage upon which to do it. After all, one “natural tendency” that Chipotle clearly has no interest in allowing the animals to display is their tendency to want to live.

Lauren Gazzola is a longtime animal rights activist. Follow @LaurenGazzola.