I also believe this will give the game a much stronger replay factor once it's completed. Different choices will lead to genuinely different outcomes, character paths, and consequences, rather than simply changing a few lines of dialogue before converging back to the same result.
In future updates, you'll have the option to simply not pursue a relationship with Caleb at that point. If you choose that route, Nyra won't attack him, meaning neither of them ends up dying during that encounter.
So there will eventually be a path where both Caleb and Nyra survive, but it will come from avoiding the situation entirely rather than resolving it after the confrontation begins.