The reasoning of "it's a rape joke because rapists say it" is flawed. Rapists could say plenty of other things (e.g. "shut up") which, if repeated, aren't considered to be rape jokes; and there are situations where "just let it happen, it’ll be over soon" could be said in a non-rape situation, e.g. smothering someone (or even something less serious, like getting a tattoo).

I'm not going to make a comment about whether or not I consider this to be a rape joke, but I wanted to comment on what I consider to be an incorrect leap in logic.