How precisely did you disable it in httpd.conf file? If you uncheck FollowSymLinks in WHM > Apache Configuration > Global Configuration area and save that setting, then you should have httpd.conf change to the following:
The setting for <Directory "/"> should not be able to be overrode by any user's .htaccess file.
Options ExecCGI Includes IncludesNOEXEC Indexes SymLinksIfOwnerMatch
Options Includes Indexes FollowSymLinks
Allow from all