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.
You had mail. Paul read it, so ask him what it said.