I think one flaw in their reasoning comes here:
Players often say that they're making alliances or waging war against Cleopatra, Gandhi, or Montezuma - not Egypt, India, or the Aztecs. (emphasis added)
When the civs were linked to the leaders and it wasn't even conceivable to think of the apart from one another (as they were 1-6)* one could use either way of
referring to the civ and it would amount to the same thing. In circumstances like that, the tendency might even be to favor the leader name, because our minds more easily conceive of agency in connection with individual human beings.
But of course, whenever anyone said "I am waging war against Cleopatra," they
meant "Egypt as led by Cleopatra," since one wages war against a country, not an individual human being. "Cleopatra" was serving as a shorthand (a synecdoche), all the more in that she lived for millennia, which no
person does. When you imagine the entity-against-which-you-are-waging war, what is in your
mind is actually the country (whichever of the two options for
naming it you might use), if only because it is a map-territory to which you will be sending troops, and if you are successful, some segment of that map-territory will now be contiguous with your own (in your country's border colors).
People don't play
as or
against "Ghandi," because Ghandi is not a
civilization, and that is true however it is that they might
speak about the matter.
*Edit: I've since been reminded that both 4 and 6 actually had multiple leaders with a particular civ, so my comments might be limited to the experience of someone who has mostly played 3 and 5. I still think that, even in those games, when you attack, you are attacking a state (conceived of as a territory), even if the game may have allowed for that state to have had a different person as its leader. (Diplomacy is maybe different; treaties are often worked out by (or crucially signed off on by) individual leaders.)