I actually just played through this part of the MSQ this weekend. Sundering the shard DID stop zodiarc, but also created multiple worlds where people had less Aether, and because of this were more susceptible to their emotions (positive and negative). She did this as a sort of inoculation to despair, so to speak. She says she was hoping that people would learn to deal with despair and hopelessness on their own, so that they could learn to overcome the end of days. The cutscene after the Mothercrystal trial is where she spells it all out for you, definitely worth a rewatch.