It's simple...make it so the computer can't name features! You're playing from your civilization's point of view, so, essentially, the names that other civlizations choose for a specific terrain feature might not work for your civilization. There are different names for different regions on Earth (for example, Korea uses East Sea while Japan uses the Sea of Japan). It should be up to the player that names it.
One thing that I have always thought would be cool was a "history" thing, where you could click on a city and see "created in 500 BC, captured by the Arabs in 20 AD, Copernicus's Observatory built in 800 AD, etc". You could also be able to do that for an entire civilization. This would help in the naming features thing, such as "great battle takes place on the Great Plains between 100 AD and 220 AD between the Dutch and the Americans" or whatever. It would go hand and hand in naming. Plus, in multiplayer especially, it would help in teams: "Move your units into the Great Plains and prepare to attack them" or whatever. Naming things would be an interesting choice in my opinion, and could add a bit of flavor to the game.