So what do current systems do?
* Go for broke, go full threading (eg. HN, Reddit, Usenet).
* Ignore it (eg. phpBB). Just like real life, everything gets muddied, but you have far more people in the conversation that would be practical in reality.
* Track it but try to hide it (eg. Twitter). Discussions have tree structures, but you can only have a flat view of them. You have to manually sift through replies to find the branching points and then trace it from there.
For example, these are two discussion trees branching from the same conversation starter:
https://twitter.com/lgarvey/status/279088834115940352
https://twitter.com/nitecoder/status/279088173743747072
In any case, I suspect Discourse's threading mostly stems from Jeff Atwood's dislike of threading: http://www.codinghorror.com/blog/2012/12/web-discussions-fla...