The information from iLounge is still somewhat limited, and more specific details about the situation aren't yet available. At the surface, though, it seems that Drivetrain, which is merely a remote control for the Transmission torrent client on Macs, is currently on Apple's blacklist. If Apple wants to go that far, they might as well restrict torrent apps on the desktop or say that VNC clients aren’t allowed, since they could be used to remote control pirating machines.
Ultimately this is all coming back to the same point: Apple wishes to retain total control over the iPhone, which they see as their phone – not the user’s phone. It is a pity, as they have crafted one of the most unique and important modern computing devices. Why impose artificial restrictions on yourself or your users?