Have you got Settings > Safari > Block Pop-ups 'on' ?
You may also want to clear Safari's cache : Settings > Safari > Clear Cookies And Data and also Clear History
And close Safari via the taskbar and do a soft-reset and then see if the popup reappears when you re-open Safari. To close Safari : from the home screen (i.e. not with Safari 'open' on-screen) double-click the home button to bring up the taskbar, then press and hold any of the apps on the taskbar for a couple of seconds or so until they start shaking, then press the '-' in the top left of the Safari app to close it, and touch any part of the screen above the taskbar so as to stop the shaking and close the taskbar.
To do a soft-reset : press and hold both the sleep and home buttons for about 10 to 15 seconds (ignore the red slider), after which the Apple logo should appear - you won't lose any content, it's the iPad equivalent of a reboot.