Handling as much as you can, every chance you get isn't going to do anything for a ball
python. They're docile by nature, although I have heard of a few nippy fiesty ones, it isn't common. Babies are just going to be more afraid simply because they are babies. They don't know that you won't harm them, for all they know you could be preparing to eat it. Less handling and shorter time periods, until she gets older and calmer.
Also, is she eating consistently, handling too much can cause her to stop eating because it's too much stress.