Mankind encounters an alien race of herbivores, who regard all flesh-eating creatures as an abomination. The aliens may be herbivores but they are NOT pacifistic; they are fanatical militants determined to erase all flesh-eaters from the universe.
In a way. IIRC, Vulcans (from Star Trek) are all vegetarians. And yes, most do regard us humasn as filthy, abhorrent, beasts who let out emotions get in the way of proper, rational, thinknig. At least that’s the impression I got.
“He was a scrawny calf, who looked rather woozy
No one suspected he was packing an Uzi
Cows with guns”
from Cows with Guns, a song…not really Sci-Fi but funny as hell.
I seriously dont think this exact idea has been covered but its really no different than any alien race with an agenda to wipe us out for whatever reason. If you could sustain it I think the read would be a great comedy though.
Sounds like the K’Kree from Traveller. See http://www.rpgunited.com/product/gurps/6607.html
Not exactly the same, but in Jack L. Chalker’s Web of the Chozen a race of herbivores on a planet turns out to be humans transformed by a genetically-engineered virus. When their survival is threatened, they decide to infect the rest of humanity with the virus, turning everyone into alien herbivores.
Chalker opened the bookm with a recounting of a supposed meeting between Mark Twain and George Bernard Shaw at a meeting of the latter’s Fabian Society. After listening to descriptions of the Fabian Utopia, Twain commented “Sounds like a herd of cows after they shot the last wolf!”
Never heard this story before or since, or anywhere else. But apparently it inspired the story.
Can’t remember the name of the story or the author, but I remember one novella where a telepathic vegetarian visits earth. Turns out eating meat is wrong, even for animals. So the aliens set up a telepathy dealie where if you kill you experience the same thing as the being you kill. Which means humans are now forced to become vegetarian, but every carnivorous animal (above some sort of neurological complexity) will go extinct. Humanity faces an ecological catastrophe, saved only because the vegetarian federation sends food.
The really annoying part was that the author seemed to think the alien’s plan was a good idea.
In Piers Anthony’s Orn/Ox series (whichever the one with the flying manta rays was), the main alien species that the humans encounter is herbivorous and considers the meat-eating members of the human exploration party to be inferior (or at least dislike them enough to only hobnob with the one vegetarian, who also happens to be the science geek).
Pierson’s Puppeteers KINDA match your idea, though it’s a litter different:
The Puppeteers are an intelligent race of herbivores who uplift humanity as a foil for the even more carnivorous, even more dangerous kzinti. Their plan is for humans to best the kzinti in the wars two such predatory species are sure to (and do) have, and then they can manage the humans while the humans manage the kzinti. Very subtle.
Sounds like “Rule Golden” by Damon Knight. A farfetched but interesting story, which argues that all governments - even democratic ones - are ultimately based upon the threat of force. When no one can hurt or kill someone else without feeling it, human society as we know it collapses.
In “Childhood’s End” by Arthur C. Clarke, the Overlords do something similar: they make everyone watching a bullfight in Madrid feel exactly what the bull feels. And so ends a longstanding Spanish tradition… 
You can have my Big Mac when you pry it from my cold dead hands you filthy vegan alien.
Anne McCaffrey did something like this with the Thekk (?) race. To join their galactic hegemony, you had to give up evil, meat-eating ways. If you didn’t, the Thekk might sit on you. And since they were 800 ton pyramid creatures, that tended to hurt.
I believe they appeared in “Dinosaur Planet” and a few allied books. IIRC, that is.