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.
<Directory "/">
Options ExecCGI Includes IncludesNOEXEC Indexes SymLinksIfOwnerMatch
AllowOverride All
</Directory>
<Directory "/usr/local/apache/htdocs">
Options Includes Indexes FollowSymLinks
AllowOverride None
Order allow,deny
Allow from all
</Directory>
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