I've been an air pollution control lawyer for almost a quarter century, mostly prosecuting big companies like Chevron, etc . . . , but I also work on the little stuff, like the gas station owner who doesn't keep his vapor recovery equipment in proper spec. I wish I had a nickel for every time I heard the "why don't you stop cows from farting" argument. The best science we have indicates that, basically, lots of people doing lots of little things adds up in a big way.
As motorcyclists, I think we can all feel good about being friendly towards the environment. You're generally getting better MPG than a car and, maybe more importantly, contributing very little to road congestion. Just don't kid yourself that when remove the evap canister or the cat converter that it's an environmentally neutral action.
I've changed pipes on most of the bikes I've owned, so I'm not taking a holier-than-thou position here. These days, I do commute on a Brammo Empulse. It's a nice feeling, and it does the job better than any ICE bike.