Access to popups is not currently exposed in `39`. The next version (`41`) will expose much more of the underlying `CEF API` and provide that functionality.
Version `41` is a work in progress you can check it out at
https://github.com/cefsharp/CefSharp/tree/cef/2272 though the `API` is yet to stabalise, so be warned.
There are still likely a few missing pieces to implement before what your attempting to do will work properly.
For reference `OnBeforePopup` is called before a popup is created, so it's too early to execute script on a popup.
Can you reference the popup in javascript? Like get a handle to it's window object and access it's elements? (Been a while since I toyed with popups in javascript, so I can't provide any specifics.).