Since this cannot be fixed on your end, I, personally, would prefer that those pets not have their rarity counted towards the pet score. At least that way, those of us who have
upgraded our non-battle pets would not be bothered by the discrepancy.
I don't know why Blizzard even gives those pets a rarity in the first place... and since the rarity of those pets does not really matter (except to those of us who like to see all blue pets
), I doubt that they will ever bother fixing it.