There should be a method for renaming a pet. Its quite irksome to get a pet from a quest reward or boss drop and to have a really bad name. I just completed the Penny Dreadful quest and my cyclops is named Sassy.... And theres no way to get another replacement cyclops.
If you're not happy with your pet's name, you can now choose a new name by going to the Dye Shop in the Wizard City Shopping District. You will see an icon there that will instruct you on how to rename your pet, for a small gold fee.