I think (since this sort of thing is weirdly relevant to my interests) that the problem isn't the threads going off topic, but that there's no effort required to see those threads. Because the topics of threads are relevant to the people participating in that discussion, just not necessarily to people viewing the topic from the root, penalizing those comments, to me, seems counterproductive unless the comments are obviously trolling or completely unrelated to the point.
That said, I think dang has mentioned penalizing off-topic comments before so it does seem like something they can do.
This may be solved by folding the threads by default. Presumably, the root comments are addressing the original post directly, so they will be the most on topic. But requiring users to take the (minimal) effort of opening a subthread to view it means only people who are interested in reading further will ever read it. Currently, having to scroll past and ignore threads you're not interested in appears to be causing a lot of friction.
Since the staff has mentioned wanting to add thread folding anyway, mentioning this is kind of moot i suppose.