This is quite complicated, but I'll try to explain!
A "pest ban" was an official declaration that someone had the plague, i.e. the red death in this case. Pest (or pestilence) was an old word for plague (even now, it is used to mean plague in other languages, e.g. "la peste" means "the plague" in French) and anyone who was declared to have the plague was banned from getting too close to other people, hence the "ban" bit.
Here, Poe is saying that the scarlet stains made it so obvious that people would avoid the victim even if he hadn't been officially declared to have the disease. So a modern equivalent might be "The scarlet stains on the body and especially on the face of the victim made it so obvious that he had the red death that people would shun him and he was unable to get any help or sympathy."
Ban in the singular is correct because although there are many stains, they imply one overall thing. (if that still doesn't make sense, please add a comment or message me and I will try to find a way to explain more clearly with an example)
Coincidentally, I am writing this in Richmond, Virginia, where Poe spent much of his life, and there is a statue of him at the Virginia State Capitol just around the corner. Sadly, that doesn't give me any extra insight though!