I'm so sorry she hurt herself!
I'm glad she's alright though!
Any time my little Eury plays a bit too hard and hurts herself, as puppies are apt to do, she also cries loudly and runs off to hide. What I generally do is scoop her up and cuddle her close. Now it seems she comes to expect it and won't stop crying until I scoop her up.
I have a feeling your little one will be just fine and won't continue to be scared of you or anything so I wouldn't worry! As long as we love them and are kind to them, dogs don't hold grudges!