I don't think it would be a problem to modify the script as I've done.
But, I'm not a linux guru..may be this modification could induce some other problems..

The fact is that I checked the /etc/init.d/networking of another debian system (agnula) wich I run too..and it is the SAME file ! So, it is not buggous, because with agnula I don't have this network problem.
The problem is coming from somewhere else..but the modification I've made in the script just works for me..
If somebody could evaluate the consequences...

I don't know if you saw the modified script. Here it is again : 

For info, the solution I adopted for now is modifying the
/etc/init.d/networking script as so (i just give the changes in comments) :

case "$1" in
start)
        process_options
        log_action_begin_msg "Configuring network interfaces"

        ###### JULIEN'S ADD (ifdown -a) #####
        ifdown -a
        if ifup -a; then
            log_action_end_msg $?
        else
            log_action_end_msg $?
        fi
        ;;


stop)
        if sed -n 's/^[^ ]* \([^ ]*\) \([^ ]*\) .*$/\2/p' /proc/mounts |
                grep -qE '^(nfs[1234]?|smbfs|ncp|ncpfs|coda|cifs)$'; then
            log_warning_msg "not deconfiguring network interfaces: network

shares still mounted."
            exit 0
        fi

        log_action_begin_msg "Deconfiguring network interfaces"
        ##### JULIEN'S REMOVE --exclude=lo #####
#       if ifdown -a --exclude=lo; then

        if ifdown -a; then
            log_action_end_msg $?
        else
            log_action_end_msg $?
        fi
        ;;

force-reload|restart)
        process_options
        log_action_begin_msg "Reconfiguring network interfaces"

        #### JULIEN'S REMOVE --exclude=lo ####
#       ifdown -a --exclude=lo || true
        ifdown -a || true
        if ifup -a --exclude=lo; then
            log_action_end_msg $?
        else
            log_action_end_msg $?

        fi
        ;;

Ciao.