After you have kept Mbuna for awhile, and restack your rock structures enough times you will know where they will dig before they do it! I actually start the digging process for them when i restack my rock structure. When you know where they will dig ahead of time you can somewhat control it, or minimize it. They dont usually dig just for fun - its usually to either open a passage or create space for a purpose (spawning?)
What I do is open up the spaces between (or under) rocks so there is enough room for a fish to go in and turn around. Its not often that I see them digging much unless I forget to open up an opening enough for them.