Aye, this question had crossed my mind at one point, but I managed to ignore it. I offer three possibilities:
a) The city levels are a security feature in the same vein as a graphical captcha
b) The city levels actually just contain power systems, not individual rays, and only one is required to operate the single Tantalus ray.
c) The levers in the city levels are an emergency option, in case the plan needs to be set in motion swiftly.
I imagine Mort took pride in giving his enemy the option of destroying the very thing he was trying to save.
Though one must wonder just how badly Mort wanted to destroy the Earth. At any one time, destruction of the Earth was easily a matter of seconds away, yet even after Keen has infiltrated 7 ray centres, the Tantalus Ray is not activated.