There is no official way to remove hd from monsters as far as I'm aware without level draining or something. You could just take the base Yellow Chocobo and make one with less HD (technically templated animals can't be animal companions depending on how "official" you're being).
Off-topic, Hero Kids is a good beginner rpg for kids if D&D is too complicated for him. Still very rules oriented, just less fiddly. phaedrusxy runs a D&D game for his 9 year old son so it's obviously do-able.