I have disabled the Message Popup due to its' intrusiveness. Is there a way to globally change all users settings? I've gone through and noticed that everyone has "Enable New Message PopUp" enabled in their settings. 

You could do it via a SQL query.

Hi Ben,

Please make a backup of your database before running any script you find on this website.

But it would be something like:

UPDATE activesocial_User SET EnablePopUp = 'False'