As far as automated updates go, they should be requiring the user to acknowledge the "Restart now?" box, and nag the hell out of users until they acknowledge it somehow.
I would put this forward: If you run on a system where it gets slower the longer it is left on (which is almost universally from programs running on top of the OS), you should have to restart for any update which changes any critical part of the OS (which I would roughly define as any piece of the OS required to get to a desktop/terminal window).
It is particularly strange that it would happen over the weekend. Updates should be downloaded and installed only on Tuesdays, unless you set it otherwise. If your scripts are running every weekend, why not set the machines to update on Mondays?