Access to a mySite can be limited using standard Apache access controls. You'll need to create a symlink to your mySiteMaker's CGI files. Then using htaccess or your Apache's httpd.conf create a <location> or <directory> entry to limit access to the symlinked directory.
Assuming mySiteMaker is installed in, "/usr/lib/cgi-bin/mySitemaker" and "/var/www/mySiteMaker":
shell> ln -s /usr/lib/cgi-bin/mySiteMaker /usr/lib/cgi-bin/secure-mySiteMaker
<Location /cgi-bin/secure-mySiteMaker/>
AuthName "(Secure mySiteMaker Access)"
AuthType Basic
AuthUserFile /etc/apache/valid_users
require valid-user
</Location>
VALID_URI /cgi-bin/secure-mySiteMaker
mySiteMaker will then compare the URI used to call the mySite with the URI listed as the VALID_URI, if they don't match, access is denied. If they do match, Apache's access control limits access.