So I got around to looking at closing old comments today, and wasn't entirely thrilled with my discoveries. The plugin that did it automatically doesn't work on MT 3.2. The plugin that did it semi-automatically doesn't work right with my data backend.
Ultimately I found a plugin that lets me close comments from a higher level menu so I can do 20 items at a time. So I went through Pic_A_Day and the Sniping Post and closed comments on everything over a month old. I think that's all I did, but if you see anything strange holler out. Also, the month cutoff is completely arbitrary, so if you were dying to mouth off on an older post drop me a note and I'll open them up.
Basically, the new spam system was stopping the comments from showing up publicly, but I was still having to deal with them under the hood. There is one reader/commenter who tends to read in bursts and comment on older entries, but I think 30 days will be enough of a window for that. Like I said, if it starts being a problem I could go to 45 days, or 60.