They don't need to make them dirty. They just up the engine size like every other manufacturer is doing these days. My 103 HO is clean and has plenty of pull at any legal or near legal speed. HD makes several liquid cooled engines these days (the 500/750 street, vrod, and the touring bikes like the ultra). One thing Harley is good at though is knowing how to sell. With a little over half the US market share they pull in about 6 billion annually. What other vehicle manufacturer has that kind of market share? Also, according to consumer reports (for what that's worth), Harley has the highest satisfaction in engine performance. It's not that the bikes are fast obviously, it's that most of the consumers of HD's aren't looking for performance type bikes. Given the small (nearly pointless) improvement in performance these enhancements give, I chalk the sales they had mostly up to people who just wanted to spend more money on their favorite toy (who doesn't want to do that?). A Harley and even a Buell simply won't appeal to someone looking for a sport/racing type of bike. The race replica market is quite crowded as it is and sadly Buells just didn't sell well (nor has any other American sport bike really).
As for the article, I suspect HD caved quickly for two reasons: one to avoid a marketing black eye if it seemed like they didn't care about the environment and two it just wasn't that big a business for them (they could afford to give it up). The manufacturers where this is their bread and butter will of course fight to the bitter end (if they have to).