I'm pretty amazed it wasn't architected this way from the beginning. Having to generate a monolithic JS file with every comment thread for every pageload for every user? Yikes.
Well, it is not for every comment thread for every page load for every user. For anonymous page views we cache the output so unless there is a new comment (or other changes to a thread) we serve cached (previously generated) javascript file.
Maybe unrelated, I just want to point out that what I don't like about Disqus is not it's speed, but that the whole display of their stuff is very cluttered.