I'll sign that partition for a separate admin script and XHTML interface (one that includes the banning, board nuking, and spamlist-changing functions in Wakaba).
How about adding flexibility to the DELETE_FIRST option in config.pl, using booleans to define when to keep or remove a thread (including AND/OR/NOT arguments)?
Also, options for both automated permasaging and pruning by postcount, creation date/time, and board position (all configurable in config.pl of course).
Some other layout points: