Why does the Torah treat forbidden relationships, even when consensual, more seriously than it treats rape?
Although all mitzvos are commandments from Hashem whose ultimate rationales are not known to us, Rambam writes (Hilchos Temurah 4:13) that we may nevertheless speculate on the reasons of the mitzvos.
Perhaps the act of sin that is between man and G-d (e.g. gilui arayos) is intrinsically sinful and the consensual aspect does not mitigate its severity. However, the act of a sin that is interpersonal (e.g. rape) is not intrinsically sinful. It is, instead, extrinsically sinful -- for if there was consent it would not be sinful at all; it is only due to the lack of consent that the impact of the act is sinful.
A similar concept is that claims or mitzvos that may be waived are not treated with the same severity and weight as those that may not be waived (איתיהב למחילה or ניתן למחילה)
perhaps because it can be rectified
Deut. 22:29 "he shall pay her father fifty shekels of silver. He must marry the young woman, for he has violated her. He can never divorce her as long as he lives"
whereas an erva makes mamzerim or forbids a wife to her husband, etc. , i.e. destroys a society if left to go rampant.