Well, depending on how advanced the pollution and pollution control systems eventually get, I throw the following ideas on the wall to see what sticks:
For players who choose not to control their pollution at all, they could simply leave the muffler hatch open to atmosphere and suffer. Perhaps the chunk gets poisoned which could affect the player's health and possibly reduce plant growth rate.
However, for players who would like to invest the time and resources necessary to control their pollution, here are some ideas that are sorta based on real life:
IRL, SO2 is one of the major emission control parameters when burning Coal. It can be removed by passing the exhaust through a scrubber that mixes SO2 with a slurry containing limestone or lime. The equations look something like these:
Limestone slurry: CaCO3 + SO2 = CaSO3 + CO2
Lime slurry: Ca(OH)2 + SO2 = CaSO3 + H2O
In GT, players could make a slurry of CaCO3 or Ca(OH)2 by adding the ingredients to water in a Mixer. Then we would need a new block called a "Scrubber". The exhaust from a muffler and the slurry would get plumbed into the Scrubber, and the Scrubber would produce CaSO3 as a dust which could be voided (or better yet, centrifuged to reclaim the components). The CO2 and/or H2O could be assumed to escape to the environment with no consequence.
Similar uses for the Scrubber could be assigned for different types of pollution.
For example, when burning petroleum products (oil, diesel, gasoline, natural gas, etc), the major pollution problem could be NOx (oxides of nitrogen). (Technically, NOx is also a concern when burning coal too, so a coal burner might need to control this too perhaps.)
One method to control NOx is by using NH3 (ammonia). Technically it's probably aqueous ammonia which is NH4OH in water, so the equation would look something like this:
NH4 + NO2 = N2 + 2(H2O)
The products of this reaction could be released to the environment with no consequence.
We would need a way to make ammonia, but I'm sure there is a machine we could pick to heat N2 and H2 in the presence of an iron or iron dust catalyst. Apparently it can be made from just water and air IRL. Here is a tiny bit of info on it:
http://phys.org/news/2014-08-air-ammoniaone-world-important-chemicals.html
Carbon monoxide could also be a concern for some petroleum burners like diesel engines. This could be scrubbed by passing the exhaust through a palladium, platinum and aluminium oxide catalyst which could be slowly consumed over time. Not sure if the Scrubber could do it or if we would want another block called a Catalytic Converter.
These are just some ideas and are certainly not 100% accurate