Have you inspected her forepaw to ensure it was not possibly injured when it was stepped on? E.g., bruising/discolouring, frequent elevation off the ground, distortion, etc. It sounds like she has had a bad scare.
Two things I recommend:
1. Give her time and space to recover from the trauma. Depending on the severity of the incident and the general temperament/disposition of the rat, the time it will take to recover can vary greatly. But first, please ensure that she does not need any medical attention.
2. Find a rat friend of the same sex for her constant companion. Rats go to one another for comfort, and after experiencing a traumatic experience they re-learn trust by observing and emulating their rat companions. It will take considerably longer for a single rat to recover from an incident such as this and re-learn trust. There are far more reasons why rats need to be kept with conspecifics, but this is just one of the many.
As well, it is an unfortunate reality that the risks are considerably higher when keeping free-range rats. Rat-proofing is constant, and there are always daily risks including getting stepped on, dropping things on them, and I have heard of an incident where someone's rats fell asleep in a laundry hamper during the day and, well... I'm sure you can guess the rest. It was extremely tragic and completely avoidable. If nothing else, I would at least recommend caging her when you are not home to supervise. Putting together a rat paradise is a fun, always-ongoing project (there are threads on here from which you can draw some inspiration for spoiling your girl, such as this one:
http://www.ratshackforum.com/forum/showthread.php?t=10041&highlight=show&page=11), and you can still bring her out in your home when you can supervise. A fun and spacious rattie mansion should keep any potentially hazardous incidents to a minimum.