I really don't see this as a problem, if the name of a city should represent the actually city as it is exactly in our history should we then also be forced to build Constantinople/Istanbul at the coast? Should the Egyptians be the only civ that could build the pyramids?
For me the names of the cities just adds a bit of flavor for that specific civ, as the names they would have called their cities were they to found them.
For me the names of the cities just adds a bit of flavor for that specific civ, as the names they would have called their cities were they to found them.