She started crying immediately and said that she cant take it because it'll mess with her hormones and make her feel awful. She said that shes been temperature tracking and that it's nearly impossible for her to get pregnant right now (also something that I know isn't even close to 100%)

Just tracking one's temperature is NOT a good way to prevent pregnancy.

We've had the baby conversation and both agreed to not exploring that route for several years, her saying regularly that she would get an abortion. I know it might not be fair of me, but I can't help but feeling if she won't use Plan B, what's to say that she wouldn't change her mind about an abortion if it came to that?

This is why it's always a good idea to use two forms of bc. Tracking your temperature is tricky for young women (if they don't also track other body functions). Why isn't she on a copper IUD, has a diaphragm etc.?