I give you a different point of view.
First, I think violence is very prone to cause ludonarrative dissonance in many games (not sure what your problem is with the concept, it has an very simple definition that probably most people using it understand). The thing is, violence in video games come primarily from gameplay that is proven to work and that most developers don't want or don't know how to do alternatives to it. But, once you have that gameplay, the protagonist will come out pretty much as a psychopath from it. Therefore, any other characterization that you make of it is going to feel off for many players.
But, in my opinion, the core of the problem with TR, B:I and I guess tLoU, which I haven't played, has little to do with ludonarrative dissonace. In my opinion, the problem is that gamers are maturing and are starting to outgrow violence as the king of gameplay and plot in big amounts. Take Infinite, for example. While ludonarrative disonance may have appeared in the criticisms, the criticism that most people was actually making was basically: "I love the setting, I love the city you have built, why do you force me to shoot and shoot, when I would be much rather exploring it?". That's the core of the issue, people just require experiences that do not revolve around violence or that at least give violence less priority and the industry is unable to provide that. And Bioshock Infinite is for me the moment when this become clear.