South America had never big animals like bison etc. So people always needed to get their proteine in other ways and guinea pigs are traditional food. What you eat and what you don't eat is very much defined by your cultural background. (Just think about snails in French cuisine or pork or even sauerkraut ).

The problem is mainly how animals are treated before they get killed.

However I agree to be such a whimp in my own culture that I don't eat rabbit and even lamb although I know it is irrational. So no guinea pigs for me either. (Sometimes I say I'm a part time vegetarian )