Your scenario is chilling and spot on. The mohammedan cultists would be targets of violence and their cult centers razed. The mohammedans would demand to be protected and the only way to do that would be to put them in protective camps. If any cult leaders survive the initial violence they should be held in a separate protective camp far away from their factions fervent followers.
Yes, the cube would have to be vaporized. War, as you say, is war.
I would still like to hear from someone with some expertise what the result would be of vaporizing Mecca, Medina, and all the other so called "holy cities". What would happen to islam? Would it disolve? If the "holy cities" were destroyed would mo be exposed as a false prophet? Would they be more angry at us then they are now? Does anyone have the answers to these questions?