Interesting, that's actually one of my biggest complaints in Slack. If a discussion should be public, it should be visible. Threads in Slack are a pain to pay attention to because they're "hidden" from view in the main channel. I appreciate how MM keeps threaded messages in the channel.
This is the biggest thing blocking us from moving from Slack to MM. With Slack you have the option of replying to a message in the channel and keeping it fully visible, just by replying in the main chat, so why don't you just do that and not use threads?
Slack only recently got threads at all -- I realize it's easy to get used to them but maybe reconsider whether it's really become a show stopper. You probably would have used Slack before they implemented threads, after all...