You could disable the notification message, but I'd advise against that. The only reason being, the first time someone doesn't know they missed an important message, you're back in the same boat.
If virus' are making it through, it doesn't sound as if the virus software that is loaded to the server is picking up all the mail that comes through. Is the virus software on the server a client software or an "Exchange server" virus client?
My advise, is to look into three options.
1. Create a rule/script to remove or quarentine specific attachments, until they're verified and released.
2. Purchase an appliance to scan prior to mail getting to the Exchange box.
3. Seek out a specific virus client, designed to work on Exchange servers.
IMO, option 2 provides the greatest security and flexibility with the least amount of maintence (highest cost as well). This is followed by option 3, with option 1 being the cheapest but the most work for you and the staff that maintains this.
If you do with the appliance option, shop around a bit. But most people I've talked with promote MailFrontier, and it seems to average about 18 per license (IE Person) and about 2k for the hardware piece (provided you do the hardware and not a software/server combination).