Providing she now has clean fecals you don't have to disinfect her entire cage and it's contents daily. Once a month should be fine. Also, she can get a flare up of coccidia whether or not she contacts her own poo. As coccidia occures naturally in bearded dragon gut flora it is both impossible and unhealthy for the dragon if it is eliminated completely. (with that in mind, good to give her a probiotic now that her treatments are over to revitalize her gut flora as many of the good bacteria would have been destroyed by the coccidia treatments).
Stress can also lead to a coccidia build up in her system as well. Poor diet or lighting can do so as well. A normal unstressed healthy dragon can maintain proper balances of coccidia and other gut flora naturally. However continual introductions of coccidia from feces, contaminated crickets etc would cause an overload of coccidia. Practice regular cleaning of the cage, spot clean poo every day (or whenever he goes), completely cleaning the cage once a month or so all help to ensure coccidia doesn't reach dangerous populations.