I would really like to see Notch release the whole thing under a non-commercial license. They should set up a bug tracker, develop in public, etc., and otherwise run as a normal OSS project, with the caveat that it is not full Free Software because of the clause preventing commercial activity.
I appreciate RMS and the Four Freedoms and what it's done for software, but I think we'd see a lot more code and a lot more relative freedom out there if someone set up a precedent and a pattern for other developers to follow in releasing source while maintaining revenue stream. It's not realistic to GPL everything, as the main developer can't make any money at that point. However, it is reasonable to release the source and say either "distribution must be limited to persons with a valid Minecraft license" or go totally non-commercial and only allow freeware derivatives (without separate license).
In this age, nothing is lost by doing this; people who aren't going to abide the license are not going to abide the license anyway, and the object code is copied around and traded on pirate networks freely. So, what more is lost by providing the source to all paying customers under legal terms that forbid activity that could threaten Mojang's revenue stream? I can't say I know of anything, but the benefit would be huge.
The only protection left against any digitized good is purely legal. If something gets online and a substantial portion of people have an interest in it, expect it to be irrevocably and freely traded in violation of any terms you establish. However, anything significant enough to be a threat to Mojang's profit stream will be vulnerable to legal remedies, and no major player (i.e., no one who'd have the money to pay Mojang) will run that risk when they know they will be sued and lose. It's just easier and cheaper to pay in the first place.
If they're planning on releasing the source to the mod community they might as well just open it straight up because it's bound to get leaked anyway.