She is protected, but she gets mad because he didn't ask if he could. From the script:
ya..she said she was..but she acted like she wasn't..LOL..IT'S A TRAP!!!
Maybe she wasn't on the pill, but said so, so the MC wouldn't panic. She seems like the kind of women who is that considerate and after all what is the morning after pill for?
But yes, I would love to make her pregnant on Mom only route too. Maybe we can even go completely degenerated and might hold hands or get married.