You are absolutely correct that while the rough edges aren't that bad right now, one thing will lead to another. I'm speaking here from personal experience. When the surface of the shell is scratched, then bacteria and fungus can get in and, before you know it, you've got a serious shell infection going. My turtle was basking on a piece of flagstone last summer. It felt pretty smooth to me but it was hard and not completely smooth and it abraided my turtle's plastron, much like it has yours. The abrasions got infected and it took a couple of months to clear them up. If left untreated, shell infections can just worsen and worsen until they are fatal.
I'd replace the rocks with something smoother for the turtles to bask on. Cork bark is perfect. It's rough but soft enough that it doesn't abraid the shell and turtles like it a lot. here's where you can get some:
http://www.blackjungle.com/Merchant2/me ... _Code=WFWH
Other options are turtle docks by zoo med (you can get these at pet stores or on-line) or acrylic turtle ramps (I haven't seen these in pet stores but they are easy to get on-line from reptile supply stores.)
One advantage of either cork bark or one of the commercially produced basking platforms is that they do not take up swimming space like a rock does. The turtles are free to swim underneath them.
I wonder if there is enough water in your turtle tank. If the water is shallow enough that the turtle can bask on a rock, then it's probably too shallow. Turtles love to swim and dive and need water as deep as you can get it. Also, the more water there is in the tank the easier it is to keep clean. With either cork bark or a commercial basking platform, the platform either floats or you can adjust the level so it's above water even when the tank water is pretty deep.
So...lose the rock, get a different type of basking platform and fill that tank up. Don't, however, put so much water in the tank that the turtle can reach the edge of the aquarium by standing on the platform because then he can (and will!) escape.