Okay, I was with you for a little while (especially on sympathy for the little indie guys, even if you don't have to, throw a couple bucks in their hats if you like their stuff), until you made clear that they're downloading it from you, presumably the authorized distributor.
Especially this piece:
I've seen someone literally sit at their computer for several hours a day for several days in a row, downloading large numbers of files they couldn't possible be using normally, only stopping each time our rate limiter kicked in and blocked further downloads for a while.
So...they downloaded exactly as much as they're allowed to, and then once allowed again, started again? Didn't hack your system, didn't go off to torrent it instead? And they're doing...what wrong again? How do you know how they're using it and if such use is "normally"?
Why on Earth does your system let people do that, if you don't want them to do that? And if they're paying you for some kind of "all you can eat" service, you don't then get to tell them "Well...I meant all you can eat, unless you're REALLY hungry." If they're paying you for that service (presumably they are, I doubt you'd be terribly upset if you were giving the stuff away to start with), just be glad you're being paid. It's cash in the hat. And with how widespread pirate content is, they don't have to throw in a nickel. A similar mistake was made with DRM--you get more grief from the legal option than the illegal one! (Whoever made the statement to you about DRM is a moron, it's not effective anyway and would drive away your users.)
Now, by all means, if you want to go find out who's uploading your stuff somewhere, and go after them, I won't have a bit more sympathy for them than you will, especially if you explicitly told them not to and they turned around and told you to fuck off. But attack that end, not your users. When it comes down to it, you can't know why anyone downloaded such and such thing.