ISTM you're thinking of merging duplicate content as a punitive measure. I think of it as a mostly positive thing: I wouldn't mind seeing a discussion on SICM once a quarter--but it'd be nice to have all the older insightful comments on it readily available.
Perhaps there should be a "hard merge" that prevents duplicates from sharing the front page, and a "soft merge" that multiplexes comments from duplicates at any time range under any of the submissions?