That stuff was definitely great but they didn't commit to it. In fact, it is never brought up again. The game's story is in shreds throughout - they start with the 'I don't want to kill' and then drop it for 'Killing is easy' within 2 hours of gameplay, and neither are ever mentioned again throughout the rest of the game, in place of generic 'we have to save the world' schtick. They don't use those early ideas to explore the character. In fact, practically nothing in the game is used to explore the character. Everything in TR2013 is superficial, throwaway story beats just for the sake of story beats without any actual thought or meaningful character writing. The 'killing was surprisingly easy' thing is mentioned in that one line, then never again.
This is an absolute failure of writing. She never needs to come to terms with anything or think about anything.
Also Roth is an insultingly bad one-dimensional character with an awful, awful Scottish accent. (I'm from Scotland and nobody sounds like that.)
The Uncharted origins comparison is also totally irrelevant, because Uncharted has never tried to tell the origin story (except minor plot-related scenes in 3). But more importantly, Uncharted never felt like it had to tell an origin story, because Naughty Dog have a great grasp of what makes a great story - not origins. So they never showed us Nathan Drake's initial forays into murder, theft or crime, because we don't need to know it. The connection built up between the player and Drake is borne from how well written Drake's dialogue is - he's incredulous when something suspicious is going on, he's upbeat and jokey when things are relaxed or a trial is over, he's serious and melancholic when things go badly wrong (eg the whole middle/late Uncharted 2), they've developed a really specific lexicon and speechstyle for him so he sounds and acts like a real person. He is just a 100x better written character.
TL;DR: Naughty Dog know what they're doing, Crystal Dynamics don't.
(I still think Rise of the Tomb Raider will be a good game, just like TR2013. I just have 0 faith in their narrative capabilities. The videos we have seen before release reinforce that, with bad, off-tone dialogue and generic screams in place of solid story beats.)