Find your prefs.ini in the appropriate GC2 folder in \My Documents\My Games and edit the resolution to your desktop resolution (DisplayWidth and DisplayHeight). You may also consider changing Fullscreen to 0, for windowed mode.
For earlier versions of DL, the prefs.ini may be in the root GC2 directory (\Program Files\Stardock\TotalGaming\GalCiv2 by default).