Persuader, my perspective is somewhat different as I converted to Catholicism from atheism at the age of 19. I am currently married to a Catholic and we have 3 young children.
I can see both points of view in this thread. As an atheist in the modern world which is the dominant world view and basically goes unquestioned the vast majority of the time you have the mindset I had.
From what I read you consider yourself intelligent, educated, mature and capable of a loving relationship. Sexual activity “before marriage” is not even something that has ever even been an issue I would imagine. For most people the marriage part is irrelevant, that is seen as a commitment separate from sex. Sex is something you do because it’s normal, healthy and desirable. You also seem to express the opinion that you see your sexual relationship as the normal extension and progression of your emotional relationship. You also express the sentiment that because you got to know your girlfriend and fell in love that this gives your sexual relationship more meaning and has a certain moral dimension. Everything that you are doing for most people in most modern societies would be considered unquestioningly normal and
shrug 
no big deal. It’s how most people form relationships and it’s how most young people conduct their relationships. In the 80s when I was a teen/into my early 20s it was exactly the same. It is a mystery to you how anyone could jump in with words like “evil” and “sin” for ordinary behavior that if anything is considered healthy and mature and boringly ordinary.
Well firstly from the outset it’s important to understand that a Catholic worldview is radically countercultural to a modern secular society. A believing Catholic has a view of relationships and sexuality that is dramatically different from the norm. For Catholics the human person is sacred. Every human being, Catholic, Christian or not is sacred. In scripture the human body is called “the temple of the holy spirit”. We believe that God’s love, the Holy Spirit dwells in us and acts in us and therefore the whole human being in every part of their person is holy. In classic Catholic theology there is no division between the mind, body and spirit - we are one. Catholics respect the power of sex. Everyone knows sex feels great, we believe God designed it that way. But because we are embodied our actions of our bodies are never separate from our mind and spirit. Therefore whether acknowledged or not sexual behavior affects our mind and spirit. It has to, it can be no other way. Without getting too deep into Catholic theology the reason we believe that we should wait until we are in a sacramental union with the person we have sex with is because it will change us and do something dramatic to our minds and spirits, something that brings eternal life into the world in the form of a child.
Catholics are very earthy, the material world is not disgusting to us it is not something to “rise above” spiritually. That makes no sense as we are part of the material world ourselves. Instead we sanctify the world around us.
From what you say your girlfriend had a faith that was real and assumed as part of her life since childhood, but for whatever reason it had not reached a mature stage and she did not understand the repercussions of her actions anymore than you did. If she was as fatally attracted to you as you describe but with a mature faith she probably would have stayed a long way away. Now by having sex her mind and spirit have changed. It should be a giving of yourself forever without holding back, but instead she is trying to reconcile herself with the idea that it is just an “expression” of her love for you. An expression that must not produce a child - as it would naturally do. Children are seen in this context not as a beautiful gift from God but an inconvienience that ruins your life.
You may not see it, you may still see no logic to it (and neither may she) but your sexual relationship has taken her to a deeper part of herself and she is having to deny that she wanted something permanent, something eternal in the form of a relationship that is forever and an eternal soul in the form of a child. She may not even know any of this in the head part that knows theology but in her whole self bodily she is conflicted and miserable.
She is trying to reconcile a dominant world view that says “have sex with your boyfriend if you love him and take contraceptives” to a Catholic worldview that says “you are a precious, beautiful child of God who needs a love that is forever for your body as well as your mind and spirit.”