As far as I know, you might have a chance of bringing back a dead civ. This requires you to have NOT disabled "restarting eliminated players".
Save your scenario as a scn file, play it and capture the capital city of an enemy - cheat if you have to. That faction will lose half its cities to another, which will be a newly-made civ. Then by reallocation cities as proper, you can slowly rebuild the new civ to be what you want.
Also don't forget that you can Destroy cities very easily by disbanding them normally - Shift + D when the icon is on them.
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Machines: outthinkable YES outfightable NO.
Men: outfightable YES outthinkable NO.
Allie Cove: outfallable INEVITABLY
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