I think the colors are perfect. The "imperial" civs like Russia, Britain, Rome, China all have a tinge of red, while jungle/desert civs have either green or yellow, which suits them fine. The only one I can't figure out is Babylon.
The orange of William of Orange, interestingly, is a conflation (from wikipedia):
The French shift from arenge to orenge may have been influenced by the French word or (gold) — in reference to the colour of oranges — or by the name of Orange, France, a major distribution point of oranges to northern regions. The name of the village did not derive from the word: in Old Provençal, it was known as Aurenja, with the initial sound later shifting (McPhee, 1975) (the original Roman name of the village was Arausio and came from a Celtic water god). The village name and fruit name thus converged coincidentally, one becoming associated with the other (conflation).