That was the first thing I was going to say after reading the original post.
Using the Greenheart Games example, it's natural to look at the figures and think that you've lost 3000 sales, but it's a mistake to look at a pirated copy of something as a lost sale; in general, people will grab something if it's free and leave it if it's not. They weren't going to pay for it anyway, regardless of whether or not they were able to find a pirated copy. You're still losing sales, of course, but nowhere near 3000.
I'm not one to advocate piracy, but I also think that it tends to get overstated. Indie game devs are still able to turn a profit - they're not all going bankrupt. The success of games on sites like Kickstarter and Indiegogo also suggest to me that there are still plenty of people who want to support the devs. Popular intellectual properties are still making healthy profits; on the other hand, piracy does make for a convenient excuse when sales are down.
I guess my main point is that, if you want to get an indie project started, don't let fear of piracy be the thing that stops you. It's not some kind of hangman's noose that gets put around your neck the moment you get started. If you've got something really special then people will be happy to throw money at you.