Actually I think that might be a different issue. Even before S7, when something dropped more than about 80 meters it despawned and respawned on the nearest platform. I used that trick to collect all the NPCs from the Hyperion on a platform after the level was hidden (due to transporting to the Acheron's cargo bay). Otherwise they would end up inside the cargo bay or on one of the asteroids since they were the only remaining ground they could jump to.
The best solution is to put a platform down about 50 meters with a couple of badass Captain groups on it that will execute the "fallen" NPC, as well as the player if he falls down there.
Can you just have it be outside of the actual mission objectives and handle it on a component basis? Just have it so they need to drop the NPC to their death as the objective action (interact with console), which removes the force field or whatever they are standing on, and at the same time is set to be the trigger for the NPC to be hidden?
Actually, if you have a ceiling over the area where the NPC falls it might work anyway. Usually it seems like the NPCs move vertically to the closest platform before moving horizontally. So if you drop the NPC he should appear on top of the ceiling above where he was standing. From the player's perspective it would look like he fell to his death, but in fact he'd be up above the ceiling where he couldn't be seen.
I'd try that and see if it works, maybe you don't need to do anything. You can't have the kill objective though.