I've seen this behavior before and it's an obvious malfunction of the flagging system.
Within the existing system, a pet's flagging in general is clearly NOT intended to be independent of that of the player. A pet is an extension of the tamer, not a seperate entity. One should be able to heal a pet as though you are healing yourself, and since UO does not make a red go criminal for performing beneficial acts on himself, the logic follows that healing the pets is not a legitimate crim act either.
5 bucks says that the UO people realize that things with this are broken but it's troublesome to work through the code and get it working right. That flagging system is probably tied in with a bunch of other stuff you don't necessarily realize, such as PVM behavior of pets. They may even have to redo the whole thing to get it to work the way they want, and that's going to be a pain in the ass.
It's clearly messed up right now and the issues feed into a number of PVP situations. If you happen to be blue and standing in town with a with a red guildmate, it's possible for your guildmate to get guardwhacked for attacking your pets, even though an attack on you would have been okay. And you can't even safely rez the red guildmate afterward because it's a crim act and guards can be called on you. Funny! (not really).