If I re-call correctly, that CLI script takes some parameters found in the options set for backups.
http://yoursite/admin/settings.php?section=backupgeneralsettings
Include users check box is selected by default which means automated backups will include users. Uncheck (deselect that item), run the cli script on one course as a test and you'll see the backup filename includes 'nu' ... no users.
php backup.php --courseid=[CID#]
where [CID#] is the course ID number.
In addition, I have a little script in /admin/cli/ that creates a text file so I can find course ID's from command line:
mysql -u root -p -e "use moodle;select id,fullname,shortname from mdl_course;"> courses.txt;cat courses.txt
courses.txt looks like:
id fullname shortname
1 Moodle 27 M27
2 SA SA
4 Moodle Sharing MSHARE
After making your no user CLI backups, you'll have to go back to the settings and re-set whatever is desired for backups.
'spirit of sharing', Ken