She will get used to it. Try when she's tried? She might fall asleep while you're doing it. I know that the only thing to calm me down in the first days of doing it was for my grand-mother to sing to me during the CPT. So try having something that calms her down or keeps her distracted, like TV or a movie she likes.
Are you sure your technique is okay? Because if it's not, it will definitely hurt.
In the worst case, I guess that not sitting still and screaming bloody murder at least helps getting the mucus loose...