it clearly states on the PetStore that a horde toon will not be able to receive an alliance moonkin hatchling and vice versa. however, upon closer inspection, when you log into your character to receive the pet, rather than looting the item directly from your mail box, you instead loot a moonkin egg. i'm guessing this is so the moonkin rewarded to you from inside can be properly assigned a faction to match your toon upon obtaining.
but what if your toon were to faction change? would you receive a new moonkin hatchling of the opposite faction? if so, this could potentially mean that a single toon could have both versions at the same time. whether or not you'd be able to use both is something else. note that blizzard only states you can't RECEIVE your opposing faction's hatchling, and the PetStore doesn't mention anything about being able to USE your opposing faction's hatchling (should you somehow get one).
i'm not sure i have the guts (or the extra money lol) to test this all out, but hopefully someone will. maybe not for the sake of testing it, but hopefully by chance they will stumble across the answer and we'll all know one way or the other. :)