Bittorrent already has something much better than SSL (for this particular purpose) called Message Stream Encryption that hides the fact that it is even conforming to any particular protocol -- it is, for all outside purposes, a wall of random data from the moment the connection is opened. The only way to identify it is via traffic analysis by recording when packets are sent and how large they are, and even that can't necessarily distinguish bittorrent from other protocols that send lots of data to random people.
I would, however, recommend using SSL for tracker access when possible, as that is completely separate from the actual p2p exchange, and can be used to identify what you are downloading (by the infohash of the torrent). Oh, and of course you should be using SSL/TLS for mail and every website that supports it.
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