No, when you activate the ARCH II, the laser automatically fires on the solar panels outside, killing the soldiers, you saw the trailer 5 months ago, right?
That is the defenses, its OPTIONAL as I diverted power to the Laser and did not activated the defenses (well, I did just to see what happened and then reloaded).
You DONT have to activate the defenses, the "Arm ARCHIMEDES Plant Defense System" option is made available no matter what option you pick when diverting power (even if you pick Emergency Output Level, just that will not work for the obvious reason).
http://fallout.wikia.com/wiki/That_Lucky_Old_Sun