Advice about filter for NOOP cmd

I recently identified a problem with a client who could not get e-mail from another company site unless they turned off the SMTP filter for the NOOP command on their ISA server. Apparently the server on the other end was sending an odd string, or large number of characters. I don’t feel right about leaving that disabled, (for DoS reasons), so does anyone have a suggestion how to keep this protected and why their server would be sending what is seen as an invalid length for the NOOP command?
Thanks for your input.
Gary