Disable update popup on Windows 2012 R2
Create/Modify a GPO using the Group Policy Object Editor.
Mode 1 (only administrators have Windows Update permission)
Disable notifications for non-administrator users. Obviously non real administrators should use a non-administrators group account
In GPO Object Editor expand Computer Configuration, expand Administrative Templates, expand Windows Components, and then click Windows Update.
In the details pane, click Allow non-administrators to receive update notifications, and set the option.
Mode 2 (not all administrators have Windows Update permission)
If you have users with administration rights but they're not the responsibles of install updates you can create a new OU for that non full administrators and link a GPO on that OU.
On that GPO, expand User Configuration.
Expand Administrative Templates, expand Windows Components, and then click Windows Update.
In the details pane open "Remove Access to use all Windows Update features" and enable it.
All the users on that OU won't have access to Windows Update. Obviously full administrators with windows update access should be out of that OU.