Ok, the message LED is connected to the Southbridge, to GPIO0. You access the bits to set or clear that signal (ie: turn the LED ON or OFF) by hitting bit0 of PCI reg 91h of function zero.
I am a DOS guy, and in DOS you could write a small Assmebly file as such:
out dx, eax ; Southbridge is device 12h
in ax, dx ; get current setting
; AH is Data, AL is direction
and ah,0FEh ; clear GPIO0
or ah,1 ; set GPIO0
mov bx,ax ; save new value to write
mov ax,bx ; recall new setting, update
This is from memory, but it should be enough. Be careful not to disturb the bits of reg 90h (contents of AL) as they are the direction bits, which will already be setup correctly for you.
Note in the above code you would probably want to add some code between the AND and the OR to decide if you want to turn ON the LED or OFF the LED. To turn ON the LED, allow the OR to happen. To turn OFF the led, skip the OR instruction.
Sorry I don't know enough Linux to show you the GNU equivalent!