One could state that someone who has scripts that do stuff the users don't expect is of questionable morals
As for the thread starter: download a small file with the version number (and maybe some other tags if you need) once in a while (socket scripting or external program or whatever). Then if that number has increased, download some version.txt with the updates and show that to the user. Then you could even ask if the user wants your script to automatically update or not. Just give the user your website url if he chooses not to auto-update.