I think the original point was that historically men have been physically and psychologically dominant over women in sexual relations. The word 'natural' was brought into it in order to rebut that position.
Natural is a vague and poorly defined word and has little or no bearing on the historical reality of the male-female relationship. Perhaps rape is unnatural. Male dominance may be unnatural for all I know. (I guess it depends on whether you include some or all of the animal kingdom in your reckoning of 'natural' behavior.) History is a record of what has happened. I suppose it could be argued that man's behavior throughout history is unnatural.
I agree and that's why it is important to look beyond the use of the word and to examine the underlying arguments.
One might justify his use of the term natural to describe rape on the grounds that rape can be found to occur in nature. That same person might want to invite his reader to draw the inference that the term natural is being used in a more narrow sense - to suggest that rape is normal, understandable, even perhaps acceptable in some basic, primitive sense. And that is why it is so important to carefully examine the arguments that are being offered to justify the use of the term natural.
Rape is natural only in the sense that it can be found in nature. Rape is not natural, if by natural is meant normal or understandable or acceptable. In nearly every society, rape is a losing strategy. ;-)