Rape has been used as a tool of war for millenia. It still is. It can be used as a form of ethnic cleansing too which makes it even more unpleasant. I'm not familiar with Nanking so I can't really comment there but for more recent examples: Bosnia, Rwanda, Sudan. Not nice.
As for defending dropping nukes, or rather defending them over rape as a more civilised, humane, necessary tool of war... Looking back, both are reprehensible. Yes, I speak with hindsight and in the midst of war, horrific actions have to be undertaken. But all I can think of is the innocent lives affected by all. Rape, nukes or whatever.
I find it troublesome to discuss either. It's fucked up, man. As cringe as it may sound. It's fucked up. Yes, rape is fucked up but so are nukes, Christ.