The CTO of a service as technically interesting as Dropbox certainly knows that he can't prevent the disclosure of their proprietary protocols. So impassioned arguments about "security through obscurity" and "the futility of trying to hide protocols" aren't adding much to the discussion. Everybody understands those things. To the extent that Dropbox's protocols factor into this story, they are obviously a fig leaf.
Thus far, the only thing Dropbox is purported to have done here is to politely ask a developer to remove an application; then, presumably believing that the mirror posts were simple nerd-rage, and that the author of the application agreed with Dropbox, Dropbox's CTO filed takedowns at Github. This is not the end of the world. As has been amply demonstrated, Dropbox can't effectively suppress MIT-licensed code, and probably won't try to.
Instead, consider that maybe all Dropbox is trying to do here is establish a track record of "not wanting Dropbox to become Rapidshare". This story then is not a "PR nightmare" for them; it's the expected outcome of their actions. They are trying to communicate both through words and actions that they are going to do what they can to not be Rapidshare.
That Dropbox cannot technically keep determined nerds from trying to coerce them into Rapidshare's use case is also not worth arguing about. I think we all know that's true. But how many of us are going to go out of our way to stick a thumb in Dropbox's eye?