Yes, we have a similar issue. We've calculated the largest mail size our scripts can process (10MB in our case), then use an Exchange server rule to automatically move larger mails to a seperate folder. Also, the Exchange rule automatically replies back to the customer explaining that their mail is too large.
When I get time, I'll try writing a script to run alongside the mail parser which automatically kills mails older than a certain time period ,to prevent the mailbox ever getting stuck overnight (or when I'm on holiday

). When I get time...
Rob