Narrative mode is probably a good addition, but I think for the problem you're describing it's overkill. My main issue with the game early on was that being infected with vampirism is just a completely random death sentence. I felt the need to save before every single ghoul encounter because my holy water reserves were just far too limited to use them on a non boss encounter.
Furthermore, this turned into a habit that made me play overly cautious even when holy water became more abundant. My idea how to solve this most effectively would probably be too much work. Maybe if there was a gauge that, once full, will cause you to be infected it would feel a bit less random? Instead of just one bad "roll" you'd need several to be affected, and that could also be used as a balancing tool, with stronger vampires having a larger chance to fill the gauge or filling it by more, compared to weak ghouls. The big question that remains then is whether this gauge should empty again by itself and when. Having it drain completely after every encounter would require some tighter balancing, but having it remain until holy water is used would make eventual infection far more of a certainty. The middle road would probably be the worst. If it drained slowly while out of combat, then that would just cause players to stand around waiting.
I think you're going for difficulty with a good deal of realism, but this could still be explained by special training or treatments providing Noctornia's members a higher resistance.