Was she under any duress? Because you can't give consent under duress. Ie. If someone holds a gun to your head and says have sex with me or die and you agree, you're still being raped. Same with threats against others, blackmail, being under the influence of drugs/hypnosis etc. It doesn't even have to be a verbal threat/quid pro quo either, just to be clear. If someone is waving a weapon around or acting violently or erratically and you believe that saying no could lead to personal harm then the sex is non-consensual, ie. rape.
I haven't played the game (and don't really want to play the game just to find that particular event - when it may take multiple playthroughs and luck to find), and will take your word for it if you say that it meets all of the above criteria, but making sure rape is properly understood and tagged appropriately is something that I think is important for this forum, and worth my time to be a whiner about.