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Why? Because it's a stupid question. Asking whether it's ethical to drive a manual transmission because its gas mileage is a few percent lower than an automatic's is like asking if it's ethical to dismember the body of the person you just murdered.
Let me explain.
The ethical issues raised by the question, "Is it ethical to drive a stick?" include such themes as conservation, environmental pollution, technological advancement, and self-enjoyment. All of these legitimately raise issues of ethics in how we, as humans, deal with each other, our planet, and ourselves. But the matter of whether your car has a manual or an automatic transmission is secondary, at best, to these ethical issues.
The real issue is driving, at all.
If there are ethical issues in your choice of transmission (and we agree that there are), they are contingent upon the deeper (and far more significant) ethical issues of driving cars in general; any positive or negative that can be said about your choice of transmission applies in greater magnitude to the act of driving itself.
Fuel economy is better with a dual clutch? Bikes get even better fuel economy. Want to support the latest in fuel-saving technology? Buy an electric car, which has no transmission, generally. Want to save our planet's resources? You definitely shouldn't drive, then, and you might want to rethink where you get your food, clothes, and electronics from, too. Concerned about destroying our environment, global warming, and the like? Well, buddy, your choice of transmission has about as much impact on the big picture as a cow fart. Enjoying yourself with your manual transmission car? You're about 3 percent more unethical than Saint Automatic--on a bad day.
There is, quite literally, nothing that makes the choice of transmission in your car an ethical issue separate from the fact that you drive your car except for a recent bit of data showing manual transmission purchases are on the (very slight) rise.
Looking around the web at the responses to Sirota's Salon screed, we have responses like the thoughtful and accurate hole-poking done by John Voelcker at Green Car Reports; the dismissive and snarkily-fun rant from Jason Torchinsky at Jalopnik; the detached and neutral poll-taking by Jeff Sabatini at Autoblog Green; and the straightforward enthusiast angle by Jeff Glucker at Hooniverse, which brought Sirota's Salon article to the attention of the online automotive media.
These are all legitimate responses to the question Sirota raises, and they're all basically correct in their own way. Ethics, or as relates most closely here, applied ethics, is a field largely about the practical application of the question of what's right and what's wrong to our lives. In this case, we're dealing, at root, with the ethics of mobility.
And here we come back to that corpse sitting in the garage. By driving a car, you've already made a decision about each of the ethical questions raised by Sirota. You've decided your desire for mobility justifies the harmful side effects of operating a personal vehicle. So quibbling over the 1-3 mpg difference between a manual or an automatic (which, by the way, frequently favors the manual transmission) is like quibbling over whether it's wrong to separate the body parts of the person you've already decided it was OK to kill.
It would make as much sense (and practically speaking, much more sense) to question the ethics of more significant sub-divisions within the field of personal mobility, like driving a conventional car instead of a hybrid or an electric, or riding the bus, or riding a bike, or working your life out so that you don't require any trips you can't cover on foot in a timely fashion--and all of these things have been and continue to be questioned, with answers on both sides having merit.
But that doesn't sensationalize a newsy data trend in an offhand effort to draw eyeballs and traffic for Sirota's writing at Salon. I wonder what the ethicists would have to say about that.