Update on the way out? ie. Pop up with two options "close" and "update and close", at least this time you've already accomplished what you were after with the application.
Ideally, you'd want a system-level daemon that downloads and preps updates in the background, and either waits until the system is idle (I think Apple has some tech like this already for running Time Machine backups), with pending updates optionally installed on system shutdown (am I shutting down to save on battery, to restart, or because I'm about to leave the office and I don't care how long it takes for the system to shut down).
Here's their announcement of it from 2013: http://layervault.tumblr.com/post/50501747774/open-sourced-a...