I don't think the Amity, or any of the other Factions are strictly vegetarian. Food isn't easy to come by. The Abnegation are grateful for any bit of food they're given. They actually appear the poorest of the Factions, although they are the leaders. Since Amity are the farmers and food producers, I would think that they'd probably have the best selection of food to eat. At least it would probably be fresh food.
remember that even though the amity's grow all the food in the city most of it goes to the factionless otherwise they would starve remember how most of the city rarely has FRESH FOOD! so the people probably couldn't live if they were vegetarians because they need meat to live because it must be the most abundant food source.
Meat takes more plants to grow than just eating the plant directly so i dont get why they would be farming meat when it would take far less resources to just eat the plants used to feed the animals in the first place. Also meat is only cheap because it is heavily subsidized by the government.
THEIR MEAT IS GENETICALLY ENGINEERED. It is mentioned in Divergent, when Tris is still in Abnegation and was cooking dinner, the evening before Choosing Day. If it involved mass slaughter of animals, the Abnegation would have definitely not eaten it.