Ideally you would have updates set to run during times when the PC is not being used such as late at night or early in the morning. If your computers have hardware that allow Wake-On-LAN to function, you can schedule a Wake-On-LAN action from the Power Save Console a few minutes before the updates take place. Power Save will not shut the workstation down as long as the Client Configuration is set on the Definitions Tab to include both Disk Utilization and CPU Utilization.
The default setting of 25% for both of these options is sufficient to prevent a shutdown while the updates are running. If your computers do not support Wake-On-LAN then it would be sufficient to allow the updates to run with Power Save configured to include both Disk Utilization and CPU Utilization as criteria to determine that the workstation is active while the updates are running.