Not the only two options, nor do I think most people would choose to apologize since it's obviously her fault and you have literally nothing to apologize for. "It's cool, don't worry about it, it's not like you could know" is a normal response, if you're not angry. But to go all out with "oh I'm so ashamed, I hope you can forgive me!" is just blatantly bad writing.Actually, it's kinda believable even tho you make a good point. I mean if you ever got in that situation you have 2 options how to respond. Either apologize or get mad at her. And I'd say probably 60% will choose to apologize and continue with "WTF ARE YOU DOING HERE"
Having said that I do feel like the writing improves the further you get into the game, and is one of the better ones in the genre when it comes to writing. Maybe the developer had some difficulty setting the tone early on (as the game is obviously being developed chronologically).