I agree with MagicRat. You'll still have the friction of the extra two cylinders without the additional combustion to support it. It would be the same as if you replaced the 3.8 with a 2.5L four cylinder and kept your foot on the brake while you drove.
Engines are also timed to fire evenly. In a V6, there is ignition every 120 degrees, so it pulses evenly over the full 720 degrees of rotation in the cycle. A 4-cylinder fires every 180 degrees. If you disable two cylinders on a V6, it will operate like; bang, bang, rest, bang, bang, rest.
Not only will it be hell to program and very hard on the engine, you probably won't gain any mileage. That vehicle needs a certain amount of fuel to be burned in order to propel it based on weight and many other factors. If you disable 33% of the cylinders, you'll end up using 33% more accelerator to accomplish the same driving style which negates any gains. Add in the fact that you're dragging along the dead weight of two cylinders not doing their share of the work and you'll probably lose mileage big time.
There might be a logical alternative. The 2.3L four cylinder was used in many of the same vehicles that got a 3.8L. You might look into a swap.... or look into a diesel vehicle
