Problem is it's not really a fault with the CDRs, it does create those legs on enterprise. The only way I can think of would be to heavily modify /var/www/fusionpbx/app/xml_cdr/resources/classes/xml_cdr.php.
I do agree, it's annoying having to explain it to users, being able to filter out any calls that are a 'clone-of' might be useful.