maybe if we put in a md5sum database of viruses and refuse to run those that are viruses?
You mean worms? Viruses modify existing files and thus it's pointless to check whole-file checksums. Signature checking has significant runtime impact (say a second just to get one .exe checked), so it's not something you'd want to do each time an .exe is about to be run. Then there are many variations of signature checks, as some virii are polymorphic and so on. I'd say it's best not to reinvent the wheel, and providing a false sense of security is pretty bad.
The only real solution for the users is to run a virus scanner at regular intervals, and additionally to maybe run wine in a chroot jail (that's a packaging issue).
Cheers, Kuba