Another compromise could be to create a new user with no password (but a valid shell and home directory), and use sudo to run the commands that need to be run as root. The user will have to be added to the /etc/sudoers file (using visudo or editsudo) and fine grain control can be used here to limit the commands that need to be run.
Then you will need to set up ssh keys for the user running the admin script and the new users you have created, so that they can ssh in without a password prompt.