The way you get usable energy out of a material is by taking it from a higher-energy, unstable state to a lower-energy, more stable one, and capturing the energy released in doing so. For example, burning a piece of nice, reactive wood, to produce stable, non-reactive C02 and ash. Generally speaking, rocks are already pretty close to being as low-energy as you can get, so there's not really any way to get more energy out of them, no matter how you modify your digestion.