David Raynes has come up with yet another great plugin for MovableType. The MT-Close plugin allows you to go through your entire blog and close the entries older than "x" day. So, if you don't want people to comment on last month's posts (for example), you would set MT-Close to "30" days and let it go through and close all your posts automatically.
I don't know if this is the 100% solution for me, per se, but it certainly would help to prevent comment spam on older posts. Like Shaan, I would like to see this project further expanded to allow category-specific options.