The issue is he may never have had the right to release the derivative he did. So the original decompile/redistribution of Micecraft's code is not legal. That people said it was GPL doesn't make it so. It was an illegal distribution of copyrighted code. Mojang didn't care and didn't stop it, but it was illegal all the same. Well what that means is that if you then made a derivative of that, it wasn't legal either. He didn't have a license to distribute a derivative work and thus he can't go and declare it to be GPL.
So now the issue comes down to the part of the code he wrote. Well that is his... maybe. The problem is that his derivative was never legal in the first place. So a court could, and probably would, award control to Mojang. This has happened in music before. Someone makes a remix without permission and the work then gets granted to the original copyright owner.
If this kid pushes it, it is likely to end up badly for him. He would likely lose rights to the code, have to pay court costs and then, if they were feeling evil, could go after him for the illegal derivative work.
Basically if you make a derivative of someone's work and you don't have explicit permission to, either from them directly or via a license like the GPL, you need to be ok with them making use of that derivative if they want to, because you aren't going to win that fight. Maybe you don't think that is how it should be, but that's how it is. Copyright owners maintain control over their work, even if they choose to overlook a given violation. It isn't "protect it or lose it" like with trademark.