Obfuscating Minecraft code doesn't make much sense to me from an IP protection angle. It is one of the easier games to build from scratch once you see how it plays. Most of the magic is emergent behavior between many simple rule systems. Nothing in that source code would be much of a revelation. It's not like there's a nanite implementation hiding in there somewhere. It's mostly boring stuff like defining how pig or sheep walk through the scene and respond to various goals. The "scariest" part of Minecraft tech is probably chunk management.
That's all true now but none of it was true back in the alpha days.
And once there were mods and mod loaders built on the obscured source, it became easier to not disrupt the toolchains than to bite the bullet; I think Mojang now wants to make moving mods easier (someone somewhere has to be a bit sad that there are famous modpacks running old versions of Minecraft because it's easier to backport everything to 1.7.10 (including running on newer Javas) than it is to update mods).