We have a fairly large koi pond that needs converted to something more safe for 2 year old. It has a top and side fountain that run into it. We've wondered about removing the koi and placing a larger sized river rock in the water to where they can be walked on, allowing possibly 2" of water above rock, but still allowing the fountains to flow? Someday we'd like to use the pond for koi again. Would this work?
I agree with @stephnie that a fence / net would be the best, not to mention easiest. I would also think about a gate (or serverel) so you can introduce your child to the waterfall, and eventually the pond as they grow over the next few years.
I'm having a hard time imagining how big/small this pond is, but add a single rock to it sounds difficult, expensive, and probably permanent. You could add smaller rocks, and/or gravel to fill the pond, but it's likely not a small project.
The only things that I can recommend watching out for are the intake(s) for the waterfalls, and/or the intake for the filter system. If you block those, or they get clogged it could be headache. You might also think about bypassing your filter system or installing a smaller filter system as you're be filling much less water, and not needing to support fish.