I'm so sorry for the whole rotten situation. Unfortunately I hear the same general theme over and over from folks who work in pet stores. It's "too expensive" or "too slow" or "not part of company policy" when employees practice good hygiene, change out soiled substrates, feed an appropriate amount of food, etc. etc. etc. Not that there aren't many excellent pet stores out there, it's just that for every good one there's a whole fleet of profit-motivated stores.
Retail businesses thrive on word of mouth and good public opinion. Getting the media involved to show that the animals were not properly cared for before you came might indeed be a good way to get this manager to reconsider her position.
I should hope she's professional enough to consider things from a marketing angle rather than a personality issue. If not, you are better off in the long run not working for her. Publicity might also give you the opportunity to keep those animals from going back to the store that made them sick in the first place.