We may want to be a little careful about those options. It might help to have game options that won't make it too obvious to choose (or avoid) one or two factions. Like making an archipelago map a sure thing for the Dutch in Civ4...
Changing amounts of native life and fungus. If the amounts going to each faction remain at the same ratios, then wanton ecological disruption would be too easy when they're low and perhaps only green factions would do well when they're high. Perhaps more arithmetic differences would be better. If they're low, the number of mind worm attacks toward green factions would drop from already low to practically none, while those toward disruptive factions would simply drop from high to medium. In other words, disruptive factions still shouldn't get such a break that they excel in comparison to their green rivals. Meanwhile, if native life is high, then the amount (at least of mind worms and such) going to each faction might be more even. Amounts going to a disruptive faction would be quite high, but preferably not so high that other attributes fail to let the faction keep up with ones that choose to go green.