Covenant, as the Creator who has cast himself into his own creation, meets an innocent young woman whom he half-seduces and ultimately rapes, an act of betrayal whose ramifications spiral towards the World's End. It is, as it were, the betrayal of Diassomer Mininderain Herself, the antitype of all treacherous love. Even though Landsdrop and the history of She Who Must Not Be Named are "true" of the Land "prior" to Covenant's historical knowledge of the Land, they are ontologically successors of the rape of Lena. It is this sin that defines not only Covenant's but eventually even Linden's moral problem in the story--not (just or centrally) leprosy or parental torment or whatever.
Evidence? Two passages, first:
And second:... sickened at heart by Lena's madness, and by the imminent ruin of the Land, he [Covenant] resolves to confront the Despiser himself. [TLD, "What Has Gone Before," xvi.]
The first passage showcases a particular detail of the Land's plight that was the turning-point impetus, for Covenant, in deciding to suspend his Unbelief and save the Land. The second passage shows a priority of motivation in Linden otherwise absent from the narrative (as far as this priority being stated goes: since usually, throughout the Last Chronicles, Linden is upset over being away from Covenant or her son). The rape of Lena created Elena, who herself created the foundations of the destruction of the Earth by breaking the Law of Death, whose abuse of the Staff of Law resulted indirectly in the Staff's own destruction, which opened the door to the Sunbane, the quest for the Isle of the One Tree, the near-rousing of the Worm there, the succession of Brinn over the Theomach as the Tree's guardian, and so on and on and on. Elena, as the first soul freed from Her, inaugurates the exaltation of the Demondim-spawn, which is the outcome of the Viles' ages of planning (the androgyny of the Vile-sired is an implicit repudiation of a culture revolving around such things as patriarchy). Because of Her redemption, Covenant and Jeremiah are preserved from the final atrocity of the Despiser's violence and given the chance to help Linden recreate the Earth and its Time.But she [Linden] remembered too well what she herself had done to the first Law-Breaker. Now she considered it the least forgivable of her sins... Because of it, ... she had forsaken her husband and her son and the imminent destruction of the Earth. [TLD, "All Lost Women," 486.]
Metaphorically speaking, the issue is of the cancer in Covenant's soul. He is a leper, mistreated by the people of Haven Farm's nearby town. But he is not just a victim, he is a victimizer, and in an exceptionally terrible way. Something in his soul makes him think that at least dream-rape has appeal. The issue is not misogyny, though, but a failure of self-command, the overarching virtue in the series. Covenant "allows" his passion to override his moral awareness.
The series' constant equation of demonic possession with rape also reflects the rape of Lena as the core moral problem that Covenant and his friends are implicitly dealing with over the course of the entire story. What Linden's father did to her has rape-like qualities, as does Linden's killing of her own mother. Moreover, the incarnate entropy of the Worm would not pose a moral problem for the people of the Land if they were not given to the eternal commitment of romantic ideality. We want to be with the people we love, forever. (Not all of us do, but some of us, and enough of us even so.) If we love ourselves (and respect ourselves, too), we will want to "be with" ourselves forever, too. Accordingly, the conflict between the corruption of love and self-command on the one hand, represented in the base act of rape, and on the other the wild magic of the silver circle of Time--manifested in a wedding ring--unfolds throughout TCTC.
Wherefore not only does the Despiser desire his own freedom from what he "perceives to be a prison" (TLD, "What Has Gone Before," xiv)--as if Time is not a prison for him, in fact, but the proper place for his self-expression as the recursive brother of God--but he desires to rape himself, and the Law and God for that matter. The eternal desolation of Jeremiah's possible real world-prison would have been the form this molestation of self-command took. But therefore when Linden forgives herself for failing to forgive Elena--forgives all this by freeing Elena from Her--metaphorically Covenant is forgiven his willingness to commit dream-rape, and Despite fundamentally loses power over his soul, enough to where the personification of Despite is "struck down," readied for reconciliation inside Covenant's soul.
And then, as Lena first told Covenant (IIRC), "The soul in which the flower grows survives."