Why does the Torah treat forbidden relationships, even when consensual, more seriously, from our perspective, 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)
first of all, rape is in some ways more stringent. in that one is allowed to kill a rapist even without a beis din (he has the status of a rodef in some cases). so the premise here is not correct.
furthermore, rape 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.
In the society of those days, rape or seduction would usually happen only if the woman was somewhere outside of her house. Rashi in Devarim 22:23 says, "A man finds her in the city - if she had stayed at home, this wouldn't have happened." And in the city we assume it's seduction unless she cries out (Rambam, Hilchos Naara Besula 1:2), and it would be even rarer for her to be in the field, where we assume it's rape. (Also consider how Amnon was able to rape Tamar only by tricking her into coming to his house.)
So rape of non-relatives must have been rare (since most women stayed home) and sort of made possible by her being out and about. But relatives are at home with you, so arayos with them could have been more common, and not something they could have done anything to prevent - Ramban to Vayikra 20:17 says that's why the Torah uses the word "kicha" about them, and why it has to add with a sister "and she sees his erva", because it could happen without her even knowing about it.