Rowling's modus operandi is to plan her series very carefully beforehand.
I wonder if she wants to let her effort 'waste' in the case it will not be filmed.
So Newt continued as a book series indeed seems like a possible outcome. I've been underwhelmed by looking at the movies for the first time. But reading through blog posts at Hogwartsprofessor.com, I now know there is more going on in the story than I previously thought. But you have to dig around a lot to get puzzlepieces, reading blog posts and listening to podcasts. While with Harry Potter, you just had to read the book.
Maybe part of the reason that the Fantastic Beasts movies have lower audience turning up is because there are no books behind the movie?
After reading the blog posts on Hogwartprofessor.com, I have to the conclusion that there may be more problems between Rowling and the other screenwriters behind the scenes. Rowling writes in ring structure form, while the other screenwriters are used to the three stages formula. Then the screenwriters tell that "Rowling has to learn screenwriting", "Writing books and screenplays is not the same" (obviously). But Rowling has proven with Harry Potter that expectations of the biggest audience possible can be changed.
I am not sure if the popularity will be big enough that 'Midnight Witches' will return. It was a different time during Harry Potter, with the burgeoning social media mostly on forums, IRC and MSN Messenger. At least, that is how I experienced that time.