I think using Matrix for this is absolutely the right way to go. Does cactus conform to the threading specification? I was planning on eventually trying this myself, but felt like I should wait until the threading MSC stabilized.
We don't support any sort of threading yet, although Cerulean-style threading is definitely somewhere down the road. Although stuff like redactions and emoji reactions are a higher priority right now.
We're also keeping our eyes out for the upcoming spaces stuff. That might be useful for grouping comment sections.