The rape thing sounds silly, but it's at least understandable it could possibly happen in that sort of situation I guess. Having never played a Tomb Raider game I see no issue with her not being a confident and badass survivalist since this is supposed to be an origin story I think.
The issue is that 99% of the time, including an almost rape is bad writing, and do you really trust Crystal Dynamics not to write something crappy here? People are losing their **** because it's incredibly likely to be godawful and a cheap way to get sympathy points for Lara at the cost of decent writing. It's like a western equivalent of making a moeblob.
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Twostuck, Homestuck RPG: http://www.gamefaqs.com/boards/8-gamefaqs-contests/62168402