Let me answer this two different ways.
First, could this have been a story written by a six-year-old native speaker of English? Yes it could. It contains the exact kind of narrative structure and semantic errors that you would expect from a six-year-old writer. From this perspective there is really nothing wrong with it, as an adult can understand what your son is trying to say.
Second, is it natural English? Not really, but it's difficult to correct as I'm not entirely sure what your son means by "it was with programming". If, as you say, he means "it was a programmed game" then sure, you could replace one with the other -- but it doesn't really improve the story all that much.
If on the other hand by "world of programming" he means a "world inside a computer simulation" (which is what I think he might be saying) then your edit is not an improvement, as it changes the intended meaning.
If I was writing this as an adult, of course, I would completely restructure it to something like:
Once upon a time there was a game called Minecraft which existed entirely as a computer simulation. One day a glitch happened and it created a monster called a Creeper, which is how they got into the game.
But I like your son's version better.