This is totally ridiculous.
I honestly don't think she has a good case, using the RTF Act as her defense. She is not farming.
According to the article, she moved there four years ago, WITH the horse. Why did it take the Township that long to notify her she was not in compliance with the Zoning Ordinance? She has a very strong case using this as her defense, but it will unfortunately cost her a lot of money to defend her position.
In addition, if the township forces her (or even TRIES to force her) to remove the horse, the township BETTER do the exact same thing with EVERY other horse violation in the township.
That's not likely to happen.
I wonder how old their Zoning Ordinance is? If it was adopted during the time she lived there, she would be permitted to keep the horse - violation or not. The ordinance would have a clause permitting existing violations to stay, but she would not be allowed to "increase" the violation. In other words, she would not be allowed to get another horse, or expand her paddock.
If I were her, I would document (with pictures) EVERY other similar violation in the township, and talk with those horse owners, and explain that they might be next. It wouldn't hurt for her to have a little backup at the Board meetings...