Too many times these pop-ups happen when I'm in the middle of a combat or something where the obscured view causes a problem. I immediately click "No" just to be rid of the window.
I did join one guild early on when I was having a problem getting to that silly mirror in Tesso. It was before I knew one could dive and could not for the life of me figure out how to click on the mirror to grab it. So, someone gave me a hand, told me about diving and asked if I wanted to join his guild. Not through a pop-up, but via the chat window. That is a far better way of doing it than slapping a dialog right in the middle of the screen during, what may be, a crucial moment in the game.