I believe that you can add an entry for the virtual domain in httpd.conf that will setup the path to cgi-bin for the domain. I'm assuming that you can point it to the sym link, however I don't have time to test this. The entry would look something like this:
<virtualhost
www.domain.com>
ScriptAlias /cgi-bin/ /www/domain/subdir/cgi-bin/
ScriptAlias /cgi-domain/ /www/domain/subdir/cgi-bin/
User domain
Group domaingrp
ServerAdmin
webmaster@domain.com
ServerName
www.domain.com
ErrorDocument 404 /missing.html
DocumentRoot /www/domain/subdirctory
TransferLog logs/eulalas-access-log
</virtualhost>
Give that a try. It should work properly.