I had to do something similar and make a very friendly RetroPie console for my mother. She likes to play a few older games, but even the menus inside of emulationstation can cause games to be deleted amongst other problems.

So what I suggest is to actually dive into the emulationstation source code if you can handle it. What I did was customize emulationstation to make it super protected. I removed several features like the scraper, nearly all the options under the UI and sound menu, and under the shutdown emulationstation menu, all I left was the ability to turn it off. I set up a button that boots the system up, plays a nice little video that goes right into ES. There are no options where she can mess up or really configure anything. All she can do is select a game. I also set up the button to exit the game back to ES. Then she can shut down from ES and that’s all she can do. I had to make my system be fool-proof, and make it look as nice as possible. I went so far as to completely hide all console messages etc…

So to answer your first question, yes, you can edit and shield/filter the configuration options in ES but it takes a little work and learning how to compile the source.