Way to enable/disable individual trunks from outside of FreePBX GUI (command line, script, etc.)

I had this problem too and i have tried every possibile solution: local dns cache, force the ip address in /etc/hosts but the problem is that asterisk has a poor dns implementation. This problem is resolved in asterisk 1.6.1 (not 1.6.0), the DNS manager now run in background and perform DNS lookups asynchronously.
However you can try this script, taken from an another forum but adapted for freepbx 2.4/2.5. When internet is down it rename the /etc/asterisk/sip_registrations* files and reload asterisk. For me this resolved all hang problems.

# check if network is up
VAR=`ping -c 1 $1  > /dev/null; echo $?`
VAR2=`ping -c 1 $2  > /dev/null; echo $?`

#
 if [ $VAR -ne 0 ]; then
  if [ $VAR2 -ne 0 ]; then

    if [ -f /etc/asterisk/netup.ok ]; then
       rm /etc/asterisk/netup.ok
       mv /etc/asterisk/sip_registrations.conf /etc/asterisk/sip_registrations.conf.down
       mv /etc/asterisk/sip_registrations_custom.conf /etc/asterisk/sip_registrations_custom.conf.down
       /usr/sbin/asterisk -r -x "reload"
    fi
  fi
 else
  if [ -f /etc/asterisk/netup.ok  ]; then
     echo 1 > /dev/null
   else
      echo 1 > /etc/asterisk/netup.ok
      mv /etc/asterisk/sip_registrations.conf.down /etc/asterisk/sip_registrations.conf
      mv /etc/asterisk/sip_registrations_custom.conf.down /etc/asterisk/sip_registrations_custom.conf
      /usr/sbin/asterisk -r -x "reload"
   fi

 fi

You name this script for example:

/usr/sbin/check_wan.sh

and in crontab you add

*/3 * * * * /usr/sbin/check_wan.sh 4.2.2.2 208.67.222.222 1> /dev/null

So every 3 minutes check if two famous dns are available and if both are unreachable execute the script.

I lost the first row on cut and paste:

#!/bin/sh