I think there is a way to do this. If I recall right.
Finish laying out all the other civs and there units.
Then edit the settler unit and make it a non-settler, no move rate and a high defense. If this unit is destroyed then the whole civ is destroyed.
However, by doing this you prevent the civ from founding any cities and the original unit is not removed.
I think this worked once before in a scenario I wrote a long time ago. Try it out and see if it works.
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