There's a difference between making a joke about something, and using something irreverently. I think that a lot of the arguments made against using the word 'rape' are not about the fact that jokes are made *about* rape, but that 'rape' is used as such a throw-away term when people are trying to be funny.
I would argue that nothing should be completely off topic for humor, any more than anything should be off topic for any conversation. But I would say that there are things that we should not desecrate needlessly.
To use the common derogatory usage of the word 'gay' as en example; it's fine to make a joke based around 'gayness', but using 'gay' just as a punchline to mean something bad, is harmfully denigrating the word and those things associated with it.
It's not often I see someone make a joke that is genuinely about rape (as opposed to just using the word rape in a humorous way). I would defend the former, and whilst I wouldn't always take offence at the latter, I do appreciate why a lot of people would, and would refrain from using it. Not just because I don't want to offend people, but because I believe it can be genuinely harmful to trivialise these things through our language.
So to address the original poster, who heard that discussion of rape was harmful "even when using the word as a generic placeholder for something entirely unrelated", well actually that's exactly why it is harmful.
You wouldn't throw around genocide as a punchline if one had happened next door, so be sensitive to the fact that rape is actually a very common occurrence, and lots of your potential audience has probably had a close encounter with it.