I was unable to find a Scene.end() method...
import inspect, scene
print('\n'.join([member[0] for member in inspect.getmembers(scene.Scene())]))
The other methods are documented in http://omz-software.com/pythonista/docs/ios/scene.html and Ole said he would add docs for Scene.stop() here: http://omz-forums.appspot.com/pythonista/post/5822369738260480 If you add a Scene.stop() method to your Scene, it will be called when the user clicks the X.
The only ways that I have found to really end a Scene are to tap the X in the upper right corner of the window or to launch another Scene. http://omz-forums.appspot.com/pythonista/post/5876387541942272