re: Documentation.
A very interesting document. I hadn't heard of that before, however the order you cited didn't give total control:
In Situation of an enemy landing on the island of cuba and of its concentration of enemy ships with amphibious forces off the coast of Cuba in its territorial waters, when the destruction of the enemy is delaying [further actions] and there is no possibility of recieving instructions from the USSR Ministry of Defense, you are permitted to make your own desision and to use the nuclear means of the "Luna," IL-28 or FKR-1 as instruments of local warfare for the destruction of the enemmy on land and along the coast in order to achieve the complete destruction of invaderson the Cuban territory and to defend the Republic of Cuba.
(emphasis mine)
I would be very surprised if the commander would have found himself without the ability to talk to Moscow. The only plausible method I could see is if the US softened up Cuba with missiles and bombs before the invasion and in the softening up destroyed Cuba's communication abilities with Moscow. If the local commander lost those communication abilities, would he have been able to order a launch or would it have been too late?
-Steve G.