i think travinara suggested this over in the co-operative mining topic or at least something like it.
basically, instead of having the rocks mined to nothing and then starting a timer for them to magically reappear at full capacity, have the rocks "regrow" gradually, reversing the sequence of rock states when you mine them.
you wouldn't have to fully mine down a rock for it to regrow. after a mining action is completed on the rock, a timer would be reset. after approximately the same amount of time it now takes for a fully mined rock to reappear, the rock would begin to grow back at a relatively rapid rate.