Exactly. There would definitely be a possible betrayal plot going on - for both sides, really. The normal human soldiers could be sick enough of war and fighting (and losing) to want to catch a break by making a deal with the devil.
I hadn't considered the idea of corporations. The clones would be financing their war through their own means - ie, they'd control what's left of the industry, agriculture, technology of the world. The resistance would be, mostly, stealing. The very reason that they've gone back in time would be to stop the defeat.
I think the primary setting should be the present, with the possibility to swing 'back' to the future.