If you don't properly thread the comments then you will very much cripple the way a conversation can evolve, I run one of the largest forums and if there's one thing that absolutely sucks it's a lack of proper threading, it seriously restricts how long a topic can survive and how useful it can be.
The idea further down this chain of branching off sub-conversations has some merit IMO.
If I was trying to keep the system as "flat" as possible I would consider deciding on an arbitrary cut off point (total replies, or total "levels" of replies) that automatically forks a thread into a new topic and then in the original topic would display in a similar style to a comment but with "this comment has generated a new topic, 2 replies... load preview / go to topic")
not sure if that's explained well enough, but I think that would solve the problem.
You can even do self-reference and build an infinite stair.