It's funny because I'm learning Angular myself and was watching some video's from their channel on Youtube. The speaker mentions your exact problem in this video https://www.youtube.com/watch?v=ZhfUv0spHCY#t=1681 around the 28:30 minute mark.
It comes down to placing that particular piece of code in a service rather then a controller.
My guess would be to inject new popup elements into the DOM and handle them separate instead of showing and hiding the same element. This way you can have multiple popups.
The whole video is very interesting to watch as well :-)