Nobody gets fired for choosing SHA-256. It's the de-facto standard these days, it's the most likely to have hardware acceleration etc... I think it's a pretty conservative choice.
Furthermore I don't think hash performance is very critical for bittorrent, after all it's generally I/O bound.
Could you even exploit length extension with bittorrent? Given that it cuts files in chunks of the same size it sounds pretty hard to sneak extra bytes in there.
