Although I haven't tried this yet, you should be able to get the LED to light up on the AUX channel under software control, that is if you're developing your own software.
A paragraph from the DS2409 spec sheet for your amusement:
At power-on the device will be in the auto-control mode and the control output will be assigned to the
main output. The control output can be assigned to the auxiliary output by setting bit 6 of the status
control byte to a 1. For manual operation of the control output one has to select manual mode (bit 5 = 1).
The value of bit 7 of the status control byte will then determine the status of the control output. A 1 for bit
7 will make the transistor conducting, a 0 will turn it off (non-conducting). To change the status of the
device, both bits 3 and 4 of the status control byte have to be 0. Otherwise the settings will remain
unchanged. In any case, the status info byte will reflect the currently valid settings including the changes
that might have been made with the status control byte.