How can I make WSUS less invasive for our users?

Solution 1:

I think the most workable and least intrusive solution is to change the Configure automatic updating setting to 3 - Auto download and notify for install. That will not interrupt the user, and the option to Install updates and Shut Down will be automatically selected on the shutdown menu.

Periodically run a report of computers needing updates and wave a big stick at people who haven't done their updates.

Solution 2:

You could change "Configure Automatic Updates" to option "3 - Auto download and notify for install" -- you can enable and set a time limit for "Delaying Restart for scheduled installations"

You could also try "No auto-restart with logged on users for scheduled automatic updates installations" set to Enabled with "Re-prompt for restart with scheduled installations"