It sounds like you may need to place your broody silkie into a pen until she hatches(or is done being broody). I do not think she was pecking to destroy the egg, I think she was using her beak to claim and "move" the egg. I have watched my broodies steal eggs from one another by rolling them from nest to nest using their beaks.
Maybe she spotted the other egg and claimed it as hers and was using her beak to go put it in her nest. Could this be what is happening with your silkie?
I suggest putting her in a cage inside the coop until she is done being broody or using nestboxes they cannot see into from other nestboxes. That way she cannot look around from her nest and spot the other eggs. By putting "lips" on the ground portion of the nest, you also keep her from stealing the other eggs(or discouraging it anyway) because it is harder for them to pick the egg up and over something. I suggest the cage idea myself though, just make sure she's got food and water and "her" eggs of course. If it is a wire cage you can darken by draping something over it, so she doesn't stress trying to get out and steal easily seen eggs.
-Kim