I think this is a real concern. Any rational individual should be concerned about our planet and able to back up their beliefs with facts. I did some more research.
These figures are grams/km. hc = hydrocarbons (unburned gas etc), nox = nitrogen oxide.
2001 ktm 200 exc 
1997 cr250r 
average car in 2000 
These figures make it look not so bad. I;m not really concered about greenhouse gasses, just the nasty ones that cause cancer etc. I don't understand why the ktm 200 is 3 times more polluting than the honda 250. They both have 38mm carbs, the honda is an mx bike. I tend to think something else is going on here so I'm going to go with the lower cr250r estimates for my personal beliefs.
Compared to the car
ktm = hc 30x nox .028x
cr = hc 10x nox .005x
Notice they both produce far less nox pollution than a car per km.
Normalized for the ktm, 1 km of use produces this much pollution:
This really makes it seem like it's not so bad. It doesn't look like the dirtbikes are exponentially more polluting that the cars. Plus when you factor in the miles driven per year, the bikes would look downright clean (total pollution). This has convinced me to keep the ktm 200, run it as clean as possible and eventually replace it with a 4 stroke (or electic!) when it wears out. Thanks for the thoughts everyone. I'm going to keep the wr250r for long distance dual sport rides since it has such good mpg.