I don't think one popup should be a problem. Google says that their ad should not be IN a popup or on a page showing more than 3 (or excessive, I am not sure of this number) popups.
That was useful then. The official AdSense line is that ads can't be displayed in pop-ups and the navigation of sites displaying AdSense should not be hindered by pop-ups. If you're of the same school of thought as me, where all pop-ups are considered a tacky cardinal sin, then even one pop-up is enouigh to spoil your navigation!