I'm not sure exactly how much this helps you, but
Mail::Audit takes its input on STDIN, and the
two usual ways for remote clients to talk to mail servers,
POP3, are represented in CPAN.
It shouldn't be difficult to write a Perl script to grab
your mail and run it through whatever you please... the
difficulty, to my mind, would be getting your mailreader
to play nicely with Mail::Audit, which AFAIK only
writes to various Unixy formats of mailbox.
Update: You should be able to download a copy of
each message via IMAP, filter it through Mail::Audit
and/or friends, and based on the results keep it, move it
around, or delete it, also via IMAP (or more specifically,
The hell with paco, vote for Erudil!