you raised some good points, sexual assault and rape (or the attempt thereof) are not sexist, they are a tragic reality, and statistically, women are actually more likely to be raped by someone they know, rather than by strangers.
Male rape is also not treated with the respect and seriousness that it should be, one thing that doesn't help with all of the stigma surrounding rape, is that victims have a tendency to be ostracised by the community (especially in rural or smaller communities, where people are more likely to know both the victim and the offender) as well as the feeling of powerlessness and vulnerability, and this leads to drastic levels of underreporting. The lack of support services also does not help the victims, especially males who have suffered from sexual assault. The psychological effects of sexual assault are huge and the effects last.
Yes, alluding to rape in games is toeing a moral line, but i personally don't think it crosses it, there are several factors in the game that have to be taken into account, the ones that attacked Lara have likely not seen a woman in years and would have socially and morally regressed (think Lord Of The Flies). Though the scene itself largely seems to be more about Lara having to kill another human being for the first time, violence has become so mainstream in games it's now largely overlooked in comparison to attempted rape, which is hardly ever seen.
The fact that the attempted rape scene has been pushed into the limelight to stir up controversy is a little unsettling, though i wouldn't call it sexist.
Before you ask how I know all this, I studied this (among other subjects) during my Criminology degree.