At the moment, yes. All characters have access to all pets (regardless of faction) but only through the Pet Journal. It's still unclear if it will stay this way or if we'll only have access to our faction's pets (even through the Pet Journal).
I'm not sure how faction transferring will work because it seems like in order to add a pet to your journal, you need the actual item and learn its spell. Currently on live servers, faction transferring automatically transforms horde into alliance pets and vice versa, right? (I've never faction transferred
I don't know if that would still work with the new Pet Journal. It might work out for faction specific pets that are mailed to your toons, such as the Moonkin Hatchling, but I think we'll have to grind for the guild reputation pets. But I don't know. We'll have to wait and see what Blizzard decides to do.