I think in the situation you set out, the last two people left alive or mankind fails, in that situation then rape would still be wrong.
As a species we're social. There are many other social species but our level of intelligence has allowed us to construct far more complex societies than other animals, societies that are built to meet our social needs.
Society has grown ever more complex and with that our achievements ever greater. We have women astronauts, scientists, doctors. We immediately doubled our species intellectual output and achievements by harnessing the abilities of both men and women rather than just men. To say women are anything less than equal would in my opinion be a massive step backwards and the species would be far poorer for it.
The idea that strength alone should determine position makes no sense to me, if that was true then stronger men should be free to enslave and control weaker men. Our leader should be whoever is most talented in combat and everyone below has a place in an ownership hierarchy. If it's advancement for the species we want then we should choose hierarchy by intellect and if we did that we could very well find ourselves in a matriarchy or at least a swing backwards and forwards.
Back to the question itself, if it was just two people then there wouldn't be enough genetic diversity to save the species anyway so we might as well just dance and enjoy the swansong of the last days of humankind.