It hurts and she's scared, both by the impending pain and the memory of the injury. At eighteen months, my youngest fell against a brick planter and cut her face just across her eyebrow. In order to stitch her, the pediatrician had to wrap her to a board to hold her still and keep her hands down. That was a traumatic event - for years she was claustrophobic, and she remembers it today, thirteen years later. But what could we have done differently? It was traumatic for me, but looking back, it had to be done.
I think you're in a similar position. An index finger on a toddler or baby is so important, so easy to get infected, that you have to know it's healing. You have to do what needs to be done. You can try to distract her, but she's a baby, a learning machine, not an idiot, and that won't work twice if it works once.
Parenting isn't about the fun stuff. It's about handling the problems, and I feel for you. It's gut-wrenching for me to remember. I wish I has something good and helpful to say.