Most of the same code used by mod_virgule to manage and render article replies could be used to allow replies to diary entries. Diary replies could be rendered only when viewing a specific diary entry (and not in the recentlog or when viewing someone's page). Rendering a link saying "this diary entry has 5 comments" would require a virgule_db_dir_max call, but that wouldn't be too horrible.
Reply threading, with proper indentation, would be nice to have as well. One way to do that would be to add a parent key field to replies, and a tree would be built in memory before rendering. The existing database wouldn't need to be changed. All replies to an article or diary entry would need to be read to memory before rendering, but it wouldn't be that much more expensive than what's being done by the current code. Maybe the depth of the reply tree would need to be limited somehow.