There were changes made to the maps before BD was released (during game play balancing), and areas were cut off without necessarily being removed. The same thing happened in Divine Divinity; a river was added to the Dark Forest to cut off the south east corner and make the forest smaller, and at least one quest was removed (involving Buad's tea).
Presumably the crystal balls were required to open a locked door to proceed through the original level (a similar situation existed in the Aleroth catacombs in DD). Since the original maze levels were apparently larger, it may have been decided that that was too much hack and slash for the beginning of the game.
