The guinea pig bones were found to be from somewhere around the end of the 16th and beginning of the 17th Century. Guinea Pigs were most likely introduced into Europe by the Conquistadors.
These particular specimens differ significantly from their native Cavy relatives and are of the same type that was bred and domesticated as a food source in South America. However, based on the fact that the skeleton was intact with no damage, it is unlikely this little piggy was used for food.
Backing up this theory of guinea pigs being kept purely as pets during the Renaissance are European paintings from the same era. A number of paintings by Flemish painter Jan Brueghel depict multi-coloured guinea pigs that could only have been the result of selective breeding and domestication. Certainly much better than being on the dinner menu.