Comment 26 for bug 1724317

SOLVED.
Starting from your suggestion, having I a rtl8723be based wifi card, I made a simple test:

$ sudo su
# service network-manager stop
# modprobe -r rtl8723be
# modprobe -r rtl8723_common rtl_pci
# modprobe -r rtlwifi
# killall -9 wpa_supplicant

then shutdown: the system halted perfectly. I retryed several time, and always worked.

So, simply, I made a script in /usr/local/sbin/wireless-stop.sh:

#!/bin/bash
service network-manager stop
modprobe -r rtl8723be
modprobe -r rtl8723_common rtl_pci
modprobe -r rtlwifi
killall -9 wpa_supplicant

then an entry in /etc/init.d/wireless:

#!/bin/sh
### BEGIN INIT INFO
# Provides: wireless
# Required-Start:
# Required-Stop:
# Default-Start:
# Default-Stop: 0 6
# Short-Description: unload wifi modules
### END INIT INFO
PATH=/sbin:/bin:/usr/sbin:/usr/bin
case "$1" in
 start)
  # do nothing at start
  ;;
 stop)
  log_daemon_msg "Removing wifi modules from kernel"
  /usr/local/sbin/wireless-stop.sh
  ;;
 restart|force-reload)
  # do nothing at restart and reload
  ;;
 status)
  # no mean to ask for a status.
  ;;
 *)
  echo "Usage: /etc/init.d/wireless stop"
  exit 1
  ;;
esac

then, just symlink in /etc/rc0.d (shutdown) and /etc/rc6.d (restart):

# cd /etc/rc0.d && ln -s /etc/init.d/wireless K00wireless
# cd /etc/rc6.d && ln -s /etc/init.d/wireless K00wireless

et voilà. Shutdown and restart now works.