If people use other mods generators to avoid pollution let them be. Those aren't the ones that would actually like to deal with the challenge of dealing with pollution. It might be better for those to just turn pollution off in the configs.
Don't let other mods be something that will be on the way. Think only of GT and GT only, maybe BC, RC and some other mod that GT plays very well along with.
I agree 100% with Spwnx here;
Just a quick note about one thing: Effecting certain blocks that can be everywere in the world is really difficult to do. With that i mean mostly all the ideas about pollution effecting any sort of plant. While i hope that vanilla plants extending vanilla behavior (Trees) create events i can catch and modify, there are many other plants i can't easily access. For example the crops. To effect them, i would need to scan EVERY BLOCK in EVERY LOADED CHUNK to find them. Same with most other mod plants. To effect the IC2 Crops i only have some hope with using reflection... Doing that for every mod i would like to effect... Meh...
Well, I don't know how hard would be modify water, but turning into polluted water, would affect directly crop production.
If Polluted water keep substituting normal water, crops will grow as if there's no water.
Maybe trees growth wouldn't even be changed, as I assume they would be used for steam, that already will need clean water.