I like this possibility. It may help explain why the characters seem as strong as they are (magic included) and can influence the weather (pegasus ponies). It may also mean that that, besides being bigger, the food would grant a great deal of vitality both to the ponies and to anyone else eating them.
True but pony usually refer to a small breed of horse. They are not suppose to be bigger that 1,48 meter at the withers. Unless the guys is small the International Federation for Equestrian Sports would class Twilight Sparkle as an horse. Though there is always arguing about that among the breeders and riders ( and from personal knowledge will be really stubborn about their own definitions. )