allwillshatter "You could also call the process of redeeming her itself her punishment."
Exactly so. Redemption is a major theme of the game. All of the goddesses are being redeemed one at a time:
Ivala redeemed from her many years of imprisonment and slavery;
Mithyn redeemed from her centuries of torture and abuse from an unnamed Incubus King;
Zelica being redeemed from centuries of torture, imprisonment and slavery by the Anak;
Grynyth being redeemed from her ignorance and inability to use power responsibly;
Tertia redeemed from centuries of isolation, boredom, monotony;
Esthera redeemed from a life of boredom, futility, and a desire for death.
In the case of Grynyth, right at the beginning of Goddess Trainer, she recognizes that she has been a poor goddess, failing in her lack of understanding and overestimating of the strength of her power. During her Training, she came to recognize that she had become capable of acts of manipulation as vile as those of the deceased Incubus Emperor.