Anthrax treatment, even alternative treatments, still involves IV antibiotics (especially if it's inhalational anthrax). There was talk at one time of developing a ciprofloxacin inhaler, but I believe it's still in development. You could take that and run with it, though. Inanimate objects contaminated with anthrax spores are typically irradiated with gamma radiation, however, so you might (also) be able to devise a radiation treatment - inhaled or otherwise - that would kill the infective agent but not the patient.
Had you considered anything else, like heavy metal poisoning*, maybe? (If she can respond to drugs, she could be affected by the ingestion of heavy metals, since the body does actually require some of them in very small amounts.) Heavy metal poisoning is a medical emergency. Heavy metals - arsenic, cadmium, lead, mercury, thallium - can be inhaled or ingested, so you wouldn't have to break the skin. And symptoms can be gradual (say, for instance, she's using a coffee cup with a lead-based glaze but doesn't realize/notice it) and non-specific at first (and therefore hard to diagnose), so she could have worsening symptoms (and quite serious ones) before they figure it out. You can choose a heavy metal where the treatment, chelation therapy, is oral (ie, lead or thallium - although how she ingested/inhaled thallium might be tricky).
'Toc
*A subject treated particularly effectively in one of Wendy's stories.
