Anne really was meant to be the chosen one, not Mary.
Note that none of the witches have ever been shown to have red eyes. Anne's have grown red twice, the first time of which was accompanied by a forked tongue. This is a prequel to Supernatural
One line stood out that made me think this. Right after John and Cotton leave the woods after interrogating Rose and escaping the zombie hoard due to the efforts of Mercy and Mary, John says Cotton went into the woods a bookworm and "left a hunter". Somewhat odd choice of words, considering they captured Rose outside the woods and only drug her out there to interrogate her, and the zombies were most certainly not their choice. So they certainly didn't hunt anything in the woods. They used basic trapping for Rose, but that was before the woods, so it obviously doesn't count. The only type of "hunter" that he could be there is in the Supernatural sense of the word, which is used for anybody who fights supernatural forces, like zombies and witches. Plus, John and Mary? Involved with the supernatural? And in love? Considering both sides of Sam and Dean's family turn out to have been in a long line of supernatural fighters, one hunters and one Men of Letters, and you have more fuel for the fire. A hate for fighting witches could just be a family thing, considering how much hell they gave those two. Hell, it'd make perfect sense for Cotton to being the Men of Letters, considering their focus on research, books and intel, and John to start the hunters, considering him having more of the "oh fuck all this shit" mindset. Over time, as happens between many groups, they go from being close allies who work together to being at odds, looking down on each other. It would make perfect sense for the Men of Letters to focus on the research to better arm the hunters for killing shit. Angels (or Nephilim, Human-Angel hybrids) will eventually be introduced, and one of the main characters will turn out to have Angelic blood.
There are so many agents of Satan running around trying to take over the world. Eventually we should see some affiliates of the other side. Salem takes place on Masque of the Red Death's Gothic Earth.
Themes of dark magic, curses, and dark lords. Sounds like Ravenloft or Gothic Earth.