You can fix it with the scenario editor:
Just click on the "Editors" button on the Twilight launch menu, then select "File" and "open."
You need to find the install directory for GalCiv2. On my install, it's:
C:\Program Files (x86)\Stardock Games\GalCiv2
I suspect the install directory will probably be for most people:
C:\Program Files\Stardock\GalCiv2 or C:\Program Files\Stardock Games\GalCiv2
You can also right click Twilight of the Arnor in Impulse\My Games and select "Open installation folder."
Note: It is not the GalCiv subdirectory under My Documents\My Games.
Once you locate the GalCiv2 directory, you need to go into:
Twilight\Data\English\Campaigns\DreadLords
Open Apocalypse.gc2scenario
Select the "Win/Lose Events" tab
Select "Defeat the Dread Lords"
Click "Edit"
The "Race Elimination" button should already be selected, but it will say "If Krynn are eliminated, then victory"
Switch the first dropdown menu so that instead of "Krynn" it says "Dread Lords".