It was a marketing error.
The 'rape' scene is shown in the trailer, it would have barely registered on peoples radar what was happening if it had just been left in the game, but the developers held interviews basically boasting "We've made a much more mature and realistic Lara, she, like, totally gets almost raped dude!" Which is... a bit mad.
They didn't try to sell the game on Lara being more realistic because it was more focused on surviving and less about magical artifacts, and mummies, and ninjas with swords that could deflect bullets. They said it was more realistic because Lara gets hurt, and beat up, and broken again and again and again, and then all her friends are murdered, and she almost gets raped, and you'll want to protect and comfort this new Lara...
It was borderline perverted in the way they outlined the game, with a teaser trailer that is just concentrated scenes of Lara getting hurt, the whole game looked like one of the Saw movies, which is called gore porn for a reason.
Now that more information has come out about the game, it's clearer that there will be more exploration and survival, and it's not just a "lets make a pretty girl suffer" simulator, so the rage has died down, but for a while we didn't know that, and everyone (including me) was rather confused and upset about the disturbing direction the game was going.