This might just be a bug, but deleting a character with a pet exclusive to that toon doesn't remove the pet from your Pet Journal on the beta.
I had my friend find two pets that he didn't already know, the Blue and Yellow Moth. He then created a new character, learned both pets on that lowbie, and checked to make sure they were added to the Pet Journal on his level 85 character. Sure enough, they were there, so then he proceeded to delete the level 1 character. After the level 1 was gone, he logged back into his 85 and both the Yellow and Blue Moth pets were still in his Pet Journal. He could still summon them and everything.
I don't know if this is intended or if it will stay this way. At the moment, I'm hoping that this isn't a bug, though.
Deleting the pet upon deletion of a particular character might be the wrong way to go. Having multiple characters with unique collections (found through the companion tab in the spellbook) would mean keeping track of which pet is unique to which toon. Keeping tabs on all of that information could get messy, so letting players keep all companions in the Pet Journal regardless if the toon that learned it is removed seems like a good idea to me.
I'm trying to think of any negatives or exploitable actions that could be associated with keeping this in-game, but nothing's coming to mind at the moment.
It just seems too punishing if removing a character also means losing a pet unique to that toon.