I don't know for sure but I think it would clean just the surface or top of the pebbles only not injuring the pebbles. It definately would not clean in the edges/sides. My guess is that a wire wheel would work much MUCH better. I don't think you would be pleased with just the very tip top of the pebbles clean. This wheel is very difficult to use too. It has a lot of kick back/flying off a flat, even surface. It also wears out very fast on paint... grout, it would wear out in no time at all.
Also, you can try sanding lightly with a 60 grit orbital sander turning it on its edge to get the sides of the pebbles. And/or try a Dremel sanding tool. Tedious but that would work. Just to mention, the home improvement shows on TV say you have to replace the floor tiles (pebbles in this case). Another thing that might help is an acid cleaner. I don't know what it is called but many decades ago we used acid to clean off grout but it was only maybe a 32nd or 64th inch thick. Acid worked fast & like a charm. No matter what you decide to do it is going to take many tedious hours to accomplish this task. Be prepared & good luck!!!
If a contractor installed this floor, he is absolutely responsible for replacing the floor. Leaving any unwanted grout to dry is total incompetence. He is a rookie at best. Don't pay him!!!