Currently "account wide" really does mean account wide. You can access all of your pets, regardless of faction or server you're on! It's unclear if this is intended and how it will be upon MoP's release, though.
I just created a horde character on the PVP realm (my main collector is an alliance on the PVE server in the beta), and she has access to all the alliance pets.
As for the Moonkin Hatchling... only the alliance version is available in my pet journal atm. I don't know if that means I'd need to buy another one an open it specifically on a horde toon to obtain the horde version or what. Normally after creating a new character, you're mailed a Moonkin Hatchling of that faction right? It could just be that PetStore pets aren't mailed to toons on the beta server due to Blizzard's system not recognizing the beta servers as linked to your account.
Just to be on the safe side, though, I plan on creating a horde character and collecting all of the horde-specific pets before MoP. My collection will hopefully be merged across all characters in the expansion so I won't have to worry about it.