So understand that torrenting over tor isn't generally a good idea, mainly because the speeds aren't high and it strains the network. Also that it doesn't support UDP.
But if we look at the old paper about this on the tor website, there are a couple more issues listed, that don't seem to me like a tor-only issue.
The attack is actually worse than that: apparently in some cases uTorrent, BitSpirit, and libTorrent simply write your IP address directly into the information they send to the tracker and/or to other peers. Tor is doing its job: Tor is anonymously sending your IP address to the tracker or peer. Nobody knows where you're sending your IP address from. But that probably isn't what you wanted your Bittorrent client to send.
Because of the first attack above, the tracker learns both your real IP address and also the random port your client chose. So if your uTorrent client picks 50344 as its port, and then anonymously (via Tor) talks to some other peer, that other peer can go to the tracker, look for everybody who published to the tracker listing port 50344 (with high probability there's only one), and voila, the other peer learns your real IP address.
So what's stopping a torrent client doing that behavior with a VPN too and just sending your original ip address through a VPN if it already is an issue with tor?