I am not sure if stopping it at startup, will avoid the popup, but it seems to have worked for you. But if you wish, it is easy enough to turn off the popups. They are mostly being generated by the Action centre. I do not have any use for this facility, and have it also turned off. But if you open the "Notification Area" you can select the Action center and click " Hide Icon and Notification"
Alternatively, you can open the action centre in the Control panel and change the options for notification.
edit later. I didn't address the thread title. Several Antimalware programs are turning off Defender by default. The latest AVG, is one of such. Microsoft security essentials turns it off also, by default. If you are running a third party anti-malware, you do not really need defender and best to totally disable it through "services.msc"