Point is, the "meat" of the story could be retained while keeping it more firmly rooted in existing Trek lore.
But that's the thing... back when Niven wrote the episode in 1973, there wasn't nearly as much
"existing Trek lore" as there is now. They hadn't even pinned down exactly when the series took place, and its history was mostly unwritten. So it was easy to plug in ideas from other SF franchises. Niven did it in "The Slaver Weapon," and James Blish did it in his early TOS episode adaptations, which pretty much imply at some points that Star Trek
took place in Blish's Cities in Flight
universe (which, at the time, was the more established and mature franchise).
But since then, Trek history has been fleshed out in much greater detail by creators who weren't making any effort to keep "The Slaver Weapon" in mind, due to the ambiguous status of TAS as a whole and the legal issues with Niven's creations in particular. So today we have a Trek history that the details of "The Slaver Weapon" no longer fit into.
In short, the episode is an artifact of its time. I'm not that fond of the idea of rewriting books and episodes to force them to fit a more modern take, since I think it does them an injustice. I think they should be accepted and appreciated for what they are, what they were intended to be. And if that doesn't fit with modern continuity, so what? It's all equally imaginary anyway. The eccentricities of these early alternative takes are part of what makes them interesting, and I'd rather celebrate that infinite diversity than try to bowdlerize their unique attributes and bulldoze them into uniformity.