I think the argument was less that rape wouldn't have a place in the story and more "Let's not start the game with the haughty protagonist getting violently raped and then waking up next morning with virtually no trauma, cracking jokes with the mysterious elf girl, and already planning how to turn the orc's political landscape to her advantage".Which is weird because it fit the theme of the game just fine. You got a bunch of orcs, and Sabia acting as a "slave" in their camp, and they go on about having rape doesn't fit the game. Sounds to me like they just didn't know what they wanted the game to be out.
It makes sense for the dom route, but they also had a sub route. If you're going to have a sub route and put the protagonist in a camp full of rapists (yeah I know they aint all rapists) you can't exactly have the her be "in control of he sexuality".
But to be fair, no small part of the reason must have been fear of a patreon ban, because they went way too far. I do think having rape right at the game's intro wouldn't work very well for Sabia's character and the story, but the threat of rape would have been fitting to wisen up Sabia and the player to be careful with their decisions. Ideally, I think they should have used the old "good outcome" as the new "bad outcome" (in the original releases even if the player stalled properly, Sabia would still be surrounded, stripped and tackled to the ground, but she would be saved just a moment before getting penetrated), that way the intro's decisions wouldn't be so inconsequential (stall successfully and Sabia gets to keep her clothes on, fail to stall and she gets stripped and needs to be saved just a moment before bad stuff happen).