A hook is like any other training aid; it can be used appropriately or it can be abused when working with an animal.
Used correctly it will teach a snake that hook = no food, no hook = food. I don't use mine to drag my snakes around the enclosure or even to pick them up. Assuming it's not feeding day, if she's obviously awake and aware or even "foody" then the hook is the first thing she should encounter when your son opens the enclosure. Let her investigate it until she relaxes.
If she's not awake/aware then a gentle rub along her side or back with the hook will to announce his presence will help prevent a nip from her being startled, no different than if you're home dozing in your favorite recliner, you'd throw a fit too if you were suddenly picked up.
When it's feeding time she shouldn't encounter a hook at all, just the feeder. Eventually she will learn that when the hook comes in that she's not getting fed.
As for her growth rate, if she was underfed before that may be contributing to her problem. Retics, even SD's, grow a lot their first year and then slow down. How fast does her feeding lump disappear?