The captive women being impregnated in Duke3D was NEVER used as a blunt rape-joke.
If you killed the women (or if they died accidentally) you were PUNISHED with enemy spawns (I can think of one except to this, and that's the end boss fight in Episode 1). They were there as probably the only "serious" element to the entire game.
The last "canon" Episode of Duke3D (and I cannot believe I just used "canon" to describe a fucking Duke Nukem game) featured the aliens achieving their goal: They manage to get a human woman to birth a new queen.
Your goal is to kill said queen (which DOES have a very low-brow punchline associated with it...but it still makes sense from Duke's perspective).
What Duke Nukem Forever did was take that concept and twist it into some seriously warped attempt at "humor". It wasn't even the implied rape or forced impregnation that appalled me (if it shocks you, then you haven't seen as much sci-fi or at least as many B-movies as me; it's not an uncommon trope), it was how Duke responded to it that was just plain wrong.