So, it turns out SMF doesn't simply have a flag for thread subscriptions. Instead, it does a search of the database for all posts you might ever have made in any thread. Every single time you load the unread replies page. Yes.
To that end, I've created a new table in the database to track opt-out unsubscriptions, and I've written code to both update that table and check it when generating unread topics. All that's left to do now is create buttons for unsubscribing, and this should be set to push out.
However, since I'm quite tired at the moment, I'll wait until tomorrow to read through the code again before pushing it, so I don't accidentally break it for everyone and then go to sleep.