She just needs to adjust some.
I tried not to handle my little boy when I first got him. Of course I pet him a little bit, but when I held him and he wriggled it scared me too. So, I was always pretty quick to put him down before he got too frightened. And I tried a few things I'd read up on as well, like keeping an old white t-shirt in his cage so he could get used to my smell, giving him at least a day to get comfortable with his new surroundings before really handling him, talking softly to him while he was in his cage, giving treats (most of which he didn't want, lol). It took several days before he and I really had some serious one on one time in the restroom. Just make sure the room you take her to, is prairie dog proofed (no small spaces for her to get herself into), and also it's best if it's a small room (restrooms work well). Take treats in there with you so that she associates you with something positive. Eventually, she will feel confident enough to really investigate the place and you. Do this for a small periods of time frequently (several times a day). Each day, increase the amount of time you spend with her. I know you may be afraid at the time being, but yes, you're right when you said she did this out of fear. With time, she will not fear you; you two just need to bond first. Good luck! I hope you keep us updated on how you two are progressing.