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I am fully aware of the contents of the GPL and as someone said the spirit of the GPL can only be defined by the FSF so if you want to look past the legalese you look to what they are saying and they're saying selling GPLed software is okay. They probably wouldn't like doing it through the App Store though.
Personally I'm all for the GPL as meant to be read by the FSF but in a situation such as the one we are discussing where the authors have used the GPL but have not themselves written it so their understanding of it's spirit may have been wrong you're going to have to take into consideration what their understanding of the spirit in which they were giving you access to the code was also if you want to do the right thing instead of just the legal thing.
Unless your ethical view is that the author is not really supposed to have the kind of control granted by copyright law over their work in the first place so their opinion is not so important at this point. A valid way of looking at it as well but one that depends on ethics rather than just doing anything you can legally get away with.
Never mind Freenet for this, you could use I2P which also features in-network Bittorrent. Of course if you really want to only share the torrents with an anonymising network you'll need to do modifications but at least it'll be easier when you can use existing tracker software. TOR's hidden services would work as well I suppose.
Just hosting the tracker on one of these networks is an interesting idea. It wouldn't provide any protection for the downloaders and seeders themselves but if people aren't quite ready to sacrifice download speeds at least it would shift the attention back to the people downloading again if the indexing sites/trackers were impossible to attack. It would be a step in the right direction. I can see why no-one has done this so far though.