We've been under the threat of nuclear destruction our entire lives. From cobalt bombs to emps to neutron bombs, we already have ways to wipe out the organics and leave the infrastructue intact and yet here we still are. As horrible as your scenario is, I believe that the more devastating the technology, the less likely our great leaders will use them. Robot armies would indeed make short work of meat armies, but then it'd soon be robot against robot with us organics hiding in the shadows. The agenda is to keep us frightened and running in the squirrel cage to power the matrix, not wipe us off the face of the Earth (though, those contingencies exist, I imagine).

Meanwhile, keep writing those great scenes. Link them together and you have an entertaining story. Your writing is rich with imagery and complexity with hints of blackberry, almond and pine and a crisp finish...oh, wait. That was the Merlot I drank last night. Congratulations!