Probably the best way to go about it is create a dumbed down interface for them to work with. When they inevitably want to go outside of what you wrapped, you can either wrap the additional functionality they need, or show them how to use the underlying API.
Actually, when I was looking through stuff for him, I found a project that implemented Minecraft bindings for JavaScript with the aim of creating a friendly environment for kids. The author was an HNer and had posted it here a year or two ago. But the project had languished since then, and it struck me (perhaps unfairly) that it probably wouldn't work out of the box in all configurations. The last thing one should put in front of a kid is something that immediately frustrates them by failing in strange ways. Tools like that need to be really, really well-hammered. Which is one of the advantages of Scratch.
Even the RPi Minecraft appears to lack information about modding:
When those kinds of kids want to make Minecraft mods, we start them at the beginning, with Scratch.
A good place I think to go here would be a CraftBukkit "framework", something that would make a series of simple plugins easier to write for people with minimal programming ability.
That's how the Java camp was taught: with a game framework that required a few specific pieces of programming to fill in some blanks to make a predetermined game (a brick-breaker, IIRC) work.