Did anyone believe that Popcorn Time was going to end any other way than this? Either they were going to be shut down by their own choice, or their hand would be forced by outside litigation. Just because something is legal doesn't mean companies won't spend millions of dollars to make your life miserable because of what you built.
As I was arguing with rayiner on another thread, this is a prime example of what is wrong with the legal industry in the United States especially: shit is so complex that litigation is expensive, so people with more money than you can sue you into oblivion even if the law is on your side.
Another way of looking at it is that, as things stand now, the legal system is just another weapon the rich and influential can use to crush the little man.