sorry for your pet emergency. In my experience goldfish aren't the smartest, 😝, i'm not sure covering it will guarantee no more problems, that being said, it wouldn't actually add much weight to cover with larger rock, new rock will displace water.
Personally, I wouldn't be too concerned about a re-occurrence, hopefully they learn as i'm sure they would in nature, but if you wanted to be 100% sure, for peace of mind, i'd remove the substrate, depending on the size of the tank, a small dustpan works great, if it's smaller a kiddie sandbox shovel.