I have always thought that TC's motivations for raping Lena have never really been explained. Usually it is said that he was overwhelmed by the sensations of healing he experienced in the Land, with the idea that it made him *crazy* in some sense, at least temporarily -- such that he was dissociated from himself during the actual act of rape. I guess I have never really found this very satisfying, as it tends to let him off the moral hook. I think there has got to be something more to it.
Sexuality (particularly male sexuality) is often seen as related to aggression and dominance. In one particular book I read, "On Killing" by Lt. Col. David Grossman, the author argues that there is a sexual element to aggression, and an aggressive element to certain forms of sexuality. For instance (warning adult content)
Spoiler
I wonder how this applies to Covenant. I suppose I am inclined to see his rape of Lena as an act of aggression more than an act of insanity. If you think about his betrayal by Joan, his rejection by society (which, I believe, has a symbolically female aspect), his ill treatment at the hands of Mother Nature in the form of leprosy, and the twin insults of the perfect natural health of the Land and its denizens together with the illusion of healing conducted by the (female) forces of nature that are present both in body and in spirit (Lena as agent of The Land, which must be seen as feminine), leads to a rage and resentment that drives him to strike back at the feminine in a way that is fundamental. Murder may harm nature, but rape despises it: not only is the individual attacked, but the entire natural structure of life is destroyed. In particular, the social fabric is shredded: husband is set against wife, mother against child, clan against mother and child. What ought to be joyful is instead filled with resentment and pain. In essence, rape is the most explicit and comprehensive rejection of society that is possible. Seen this way, Covenant has been raped by fate; in revenge he rapes back in the form of Lena.
I think Covenant's rape of Lena is motivated by revenge for the cruelty of his fate. When presented with how life ought to be in the forms of Lena and The Land (can't help noticing some similarities between the spelling and sounds of "Lena" and "Land" here) -- nurturing, kind, and beautiful -- Covenant, who knows this to be a lie, is outraged beyond endurance, and he strikes back at the cruel lie in front of him. Nature is not just nurturing, kind, and beautiful: it is also cruel and wantonly destructive.
Nature makes lepers.