I would suggest that a pollution mechanic should come with a major re-balance of energy generation. Fuel fired generators producing more energy, et cetera. Maybe add a mechanic where all fuel cells decay into another item, most become fully depleted cells, and only a few can be recycled. Then the depleted cells have to be stored or else craploads of environmental damage occurs.
I don't think it would change the biome, but maybe poisoning crops in the chunk, killing mobs, rain that damages the player, poison clouds (or just areas of ground that damage you when you walk over). I have no knowledge of Java or Minecraft/forge code, so I don't know if any of this is feasible or not.
Was there a specific reason pollution was already denied?