Tox is pretty centralized and it's pretty terrible in a lot of ways, but those points aside peer-to-peer is fine. The problem with bittorrent is that it is high-volume peer-to-peer to a large number of peers. There is no problem with peer-to-peer in general.
If you want to use peer-to-peer, "decentralized" messaging over Tor, consider that a solution already exists: Ricochet
And it's not subject to all the NIH junk in Tox. Seriously just read their "onion routing" code, it is utterly horrific. It picks circuits by doing: node[i] = nodes[ rand() % sizeof(nodes) ]; which is wrong in so many ways it hurts.
