Would this be possible in a scenario?

I was just looking at this in the DLL and it looks like there is no easy way to change a civ. addPlayerAdvanced might work if you are willing to use some python.
 
You could use python to add in a new civ using addPlayerAdvanced like the Mercurians and Infernals do then give ownership to every city and unit of the Bannor to the Clan.
 
I think the last Auric Ulvin official scenario does just that. You may want to look at the way it's done there, and it's definitely python.
 
Alternatively you can gift all of the civilization's cities and units to another player. There's a function that lets you change the owner of a city, and the Domination spell is an example of how to do the same for units.
 
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