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What about minetest? It's basically a voxel game engine (like minecraft) with built in mod supprt (lua). It's open source (LGPL) so it can be modified freely. And it runs much better, especially on low-end hardware.
What about doing like Bukkit did for a while? You have a minecraft version that you don't distribute (that you download from somewhere else), and then all the mods and updates are released as patches to this "mysterious version"?