Natural ponds have some advantages over liner ponds, but I doubt that shoveling mud into your pond is going to help matters.
A flower pot or bucket filled with mud or sand and sunk in the deepest part of the pond will give your frogs somewhere to hibernate. But are you sure that the lack of mud is what killed them? I've had frogs overwinter in my pond with a relatively clean bottom. I could be wrong about this, but I think the burrowing is more for safety from predators than anything else. If all the frogs died, my guess would be that toxic gasses killed them. Did you use a pond vent or heater so the pond could breathe over the winter?