Okay, here's how I made it work in the FF mod:
I set it up so that Towns (the first size of city) go up to 12 pop instead of 6 before you need to build an aqueduct, and Cities (here's the important part) go up to 24 pop before you need hospitals....
Then I eliminated Hospitals, and changed the stats of the Zanarkand dome (what I replaced Shakespear's Theater with) so that it would not allow cities to reach metropolis size.....
Now it is impossible for cities to reach metropolis size (which generates pollution), but with a 24 pop cap, it means that you can work ever tile of a city that has 0 overlap and have 4 specialist citizens as well, elliminating the pollution and the disadvantages of not having any metropolises... Not to mention that it, IMO make the game more fun, not having to worry about building a ton of aqueducts early on in the game.
As for buildings, I have allowed the polluting production enhancers to remain (factory and coal plant), but I also added an optional tech called Wind Power, which makes the polluting improvements obsolete (so you can't build them after you research this tech), and allows a Wind Mill and Wind Farm improvements that produce 0 pollution, but have slightly less production enhancement.... In the modern age, it is the same thing; I'm going to add a tech called Green Energy that makes Makou Reactors (big polluters) and Manufacturing plants obsolete (and is also the tech that's prereq for Planet Studies, which allows construction of the SW that defends against the Meteor ICBM units I have in the game), but allows construction of Solar Pwr plants and Green Factories.
In addition, I elimiated commercial docks (I gave harbors the added ability of "increased trade in water"), and changed offshore platforms, airports, research labs and the Great Ironworks (or Bastok Metalworks as I call it in the mod) so that they don't pollute. It has, in all play test sessions thus far, worked flawlessly.... About the only pollution on the map is from volcanos and AIs building factories and makou reactors...