Oh I get it. She was reluctant at first to kill dudes and then you immediately begin killing tons of dudes. Interesting.
I seem to have totally missed that, although I will admit that I pay only passive attention to story in some games.
The story is there to justify the gameplay, not the other way around. It was Crystal Dynamics who made the mistake of leaning way too hard in to the "character" of Croft. I remember lots of interviews of them talking about how we will feel sorry for her or something, or that we will want to protect her.
I don't know the origin of the idea to wring humanity out of Laura through story instead of gameplay but either way it didn't work and it doesn't work for a game like this.
Either you have save points littering the environment, XP and weapon upgrades or you have a narrative focused, less mechanical game. I really do not think it makes sense to try and do both. But in the end who cares, its a fun game and is successful on that merit alone.