It doesn't work that way, I think you're analyzing it from the wrong direction - although you are right that there is an effect from the gear ratio. More on that later.
Picture the "cycle" that a cylinder is going through, with valves de-activated, and then with the intake runner shut off.
Valves de-activated: There is a certain amount of air in the cylinder at the bottom of the stroke. It gets compressed (taking up mechanical energy). It expands (giving back the mechanical energy). There are no pumping losses whatsoever because nothing is going in and out of the cylinder. Granted, there is a minor loss because of leakage past the piston rings and because of the heat transfer effects, but they're small.
Valves active but intake runner shut off: Start at the top of the stroke this time. Piston goes down with the intake valve open, pulling a vacuum. Intake valve closes. Piston gets sucked back up the cylinder, but there is compression occurring, so the energy you just spent pulling a vacuum on the intake port doesn't get completely recovered. Piston goes back down, pulling a vacuum again - the compression and power strokes do indeed offset each other. But then ... the exhaust valve opens, breaking the vacuum in the cylinder. Consequently, the energy that it took to pull a vacuum on the intake stroke, doesn't get recovered. In effect, this will have (more or less) the SAME losses on the dead cylinder as an active cylinder at idle with the throttle shut!
This is why ALL current production cylinder de-activation systems do it by closing off the valves.
Now, as to that gear ratio question ... you're on the right track with that one. Under certain light load conditions, if your gearbox has the capability to do it, it could be better to go in a tall gear with the engine under load and all cylinders working, than to be in a shorter gear with cylinders de-activated. The trouble is that at slow driving speeds, the power required to run down the road is so little that the required engine revs would be too low for the gearbox to be able to do it, and even if you DID provide such a tall gear ratio, the engine would be lugging and have unpleasant vibration under such conditions.
It's interesting to note that the hybrid versions of the GMT900 are using the 6.0 with cylinder de-activation rather than the 5.3 on the "normal" versions. GM claims that the bigger engine and the hybrid powertrain allows the de-activation to be used more frequently than if they had used the 5.3.
Interesting balancing act, but I'm not entirely sure I buy that, because I've driven trucks that have only slightly less weight than that, and only have 2.4 or 2.7 litres of 4-cylinder power TOTAL, with no extra cylinders to come in, and they were fine.