Desensitizing her (by just handling her feet daily, for gradually longer periods of time) will help her get over her issue with pulling her foot back.
You could get some protective boots for her feet right now too...they have ones that go up and over the pastern a good ways...this may help keep her foot dryer, and help heal the scratches (as Equestriun said, those may not totally heal until she is dry for a long time!); I have had good success with simply washing a horse's fetlocks with a good medicated shampoo daily, and applying chlorhexadine to them 2 times a day. Keeping her clean as possible is the key here, so whatever 'medication' you choose, you will want to hose her fetlocks off before you apply it. Try to trim any excess hair away from her fetlocks as well, because all that excess will keep extra moisture in, which is what you don't want...get rid of it, so that even when she's out in the paddock, if she finds a fairly dry spot, she will dry fairly quickly.
"The ideal horseman has the courage of a lion, the patience of a saint, and the hands of a woman..."