I am not familiar with any DNN-based document library that scans uploaded files at the moment, however, you may be able to load a virus scanning solution on the server and have it perform a scan on any file-level event that occurs at your document root and below.  That way, as soon as the files are saved, they are immediately scanned and quarantined/deleted if a virus is detected.  In addition, most of the larger virus scan solutions have public development API's that would allow you to perform scans on files through code.  The drawback is you would have to build your own document management module.

Here is a google search that has some good links: Antivirus API

We use this for our document upload user interface: http://telerik.com/asp-net-controls/http-file-upload/overview.aspx