Automatic updates on a server is a Bad Thing™.
Keeping your servers patched is a Good Thing™.
Invest in a test server (could be a VM) where you can verify the patch won't break anything. And make sure that you install patches on the production server manually.
If you have your servers in some form of cluster, perhaps two Win2k8 webservers for example, patch one and reboot if necessary. Make sure it's healthy, then patch the other and reboot.
Make sure to never apply Service Packs unless you plan to not remove them, too - they alter a lot of files in a one-way-only fashion.