I really don’t like that the Ubuntu update-manager opens a window when it finds that there updates that can be installed. In older versions Ubuntu showed a small icon in the top panel.
Apparently Ubuntu still allows you to do that, but you will need to call the following command:
gconftool -s --type bool /apps/update-notifier/auto_launch false
This will not add the icon to the top panel directly. You will need to wait for the next update for that.