BuildCraft Gates is your answer. Have one detect machine inventory and another emit Redstone signal to stop the incoming material.
Your solution is complicated by an extreme lack of buildcraft in my pack. I haven't tested the vanilla comparator yet, but if I really can just pipe in from the top, there is no problem.
I still think that as slow as the rock crusher is, it should be processing 9 items at a time, the way the steam oven does.