Hmm... didn't they post something to their website about looking forward to a new movie app? They even shared the name of it. It seemed almost like they pulled box office and were waiting for the new app to show up on the AppStore. I don't imagine Apple would have pulled the program for any reason on their part... what issue could they possibly take with it?
I don't remember the name, but it was pretty obvious, so I just make a habit of watching the AppStore for that sort of thing while waiting for it to appear. In the mean time, BoxOffice is running just fine on my iPhone.
Edit: Just read an article about it in which the author said he didn't know why it was pulled from the AppStore. It didn't provide a link to the home page, of course, and you can't get that link through the AppStore anymore...