Although she doesn't like to be held, you should still practice handling/restraint excercises with her. What if she got out and someone had to hold her still? What if she was seriously injured and a vet had to hold her and do uncomfortable things to her?
My puppy Azlan was (still is to a degree) VERY independent. He disliked being touched, never came to me for pats or attention, and actively disliked being picked up. He would freeze and arch his back if I ever tried.
Getting a dog used to handling is very important, so I would recommend a simple handling excercise called "gotcha!".
Sit in a chair or on the floor with your puppy in front of (on a leash if she wants to walk away)
Have some treats and gently stroke her (ear/tail/feet/chest) whilst saying gotcha! Everytime you say it, give her a yummy treat and praise her. You can move from gentle stroking to more invasive things, such as grabbing and reaching over her head (dogs instinctively dislike this).
Focus on areas the vet needs to look at, like the ears,feet,tail and mouth.