Firstly - Given how that trailer was edited together, I don't think they can claim sexual assault wasn't a theme. I suppose its possible it was unintentional, but someone at CD surely must have seen it before release and said "Hmm...this looks a bit rapey."
My impression from the trailer was Lara killed Mr. Touchy-Feely before he could rape her. She gets spotted, and pulled out of her hiding place. The guy threatens her with a gun whilst running his hand down her leg. She knees him in the groin, he grabs her and is kissing her neck, she bites him. How is that not
a depiction of a sexual assault? If it's depicted, it is a theme by definition.
Secondly - The Guardian article is somewhat thought-provoking. The author's main point seems to be that Lara currently doesn't have, and doesn't need, a vulnerable beginning or a "traumatic event" (such as rape) as a kick-starter to her later self. She makes sly references to the character being sexist
"Lara Croft has never been without design problems (or presumably back pain)..."
"Although Lara was originally best known for the remarkable size of her breasts – and that's still probably the first thing to spring to mind about her – she's grown into an interesting character, with plenty of adventures under her belt."
which I think undermines her a little and gives the article an undertone of the usual anti-Tomb Raider feminism. The physical design of the character is irrelevant to her (otherwise well made) point, that rape scenes are rarely justified. Whether this is the actual case in Tomb Raider won't be clear until release and we can judge for ourselves.
But there is no way CD can say rape isn't implied by that trailer.