Simple python script to shorten URLs in specified text files
Overall, LGTM.

Suggestions:


try ... except would look better than os.path.isfile(). Even if isfile returns True, you still may encounter an exception trying to open it (say, insufficient privileges), so you should be ready to handle exceptions anyway. Besides, using isfile may lead to a race (not likely in this code), if a file is removed right between testing and opening it.
The script spends most of the time in shorten_url, which in turn mostly waits for network IO. I'd recommend to give each invocation a thread.
Original files are destroyed. I'd prefer to keep originals intact, or at least provide an option for that. Also an ability to read urls from standard input is usually desirable.