Best option is to force encryption on all bittorrent traffic. Most clients support full protocol encryption (PE or MSE) these days, so forcing it shouldn't be an issue. For libtorrent, you'd set in_enc_policy and out_enc_policy to pe_forced.

Whether a particular client exposes this or not depends. In the case of this project... looks like upstream github.com/anacrolix/torrent does support encrypted connections. Not clear how to force it to use _only_ encrypted connections though.