I did in one of mine.. if your worried about scratches its on the bottom.. not quite sure if I understand you right.. I had some big lace rock on there it was fine
It's safe as long as you don't mind scratches on the bottom. As long as you distribute the rocks evenly along the bottom, you shouldn't have to worry about it cracking.
Dont worry youll be fine and if your really really worried about it im sure you can find something hidden to put between the glass and the rock. Good luck.