Well, I'm not too proud, but this on a cron job does what I need! If I get 
some time to dig into the sup source, I might have a stronger opinion about 
how/whether to integrate this sort of thing. My instinct is "no", sup copes 
with messages being moved around under it, and offlineimap does the right 
thing too.

#!/usr/bin/ruby
require 'mail'

BASE = "/home/mattbee/mail"

SOURCE = "#{BASE}/sup.sent"

FROM_ADDRESS_TO_SENT_FOLDER_MAP = {
  "matthew@work" => "#{BASE}/Work/Sent",
  "matthew@personal" => "#{BASE}/Personal/Sent",
  "matthew@othercompany" => "#{BASE}/Othercompany/Sent"
}

%w( cur new ).each do |d|
  d = "#{SOURCE}/#{d}"
  Dir.new(d).entries.each do |e|
    f = "#{d}/#{e}"
    next unless File.file?(f)
    mail = Mail.read(f)
    maildir = FROM_ADDRESS_TO_SENT_FOLDER_MAP[mail.from.first]
    if !maildir
      STDERR.print "Unknown From address in #{f}\n"
    else
#      STDERR.print "Moving #{f} to #{maildir}\n"
      File.rename(f, "#{maildir}/cur/#{e}")
    end
  end
end