I have a large blackmoore as well (he's my avatar) who has a bad habit of getting rocks stuck in his mouth. I've seen it happen at least three times, and I'm sure it goes on when I'm not looking too!

I use tweezers to get them out, but soon I'm going to have to do like you and cover all the pebbles. Flat river rocks are great for aquarium bottoms, I get mine at Wal Mart but I've seen them in craft stores too.
I'm about 90% sure that a goldfish will 'drown' if the rock stays lodged, because they take water in through their mouths to pass over their gills for oxygen exchange. If enough water is passing through, I think they'll suffocate.