You seem to have a pretty good handle on things. I don't have any suggestions to make because I think you are doing exactly what you need to: thinking things out, searching deeply, asking yourself the hard questions...
I know what you mean about this fundamental change in your core beliefs, the shift in the way you process... everything. It can be the most freeing and enlightening place to be in - or you could just hurt yourself.
This girl sounds like she's worth it. Work on all this together with her. You seem pretty receptive to whatever lessons you could possibly learn from this, and I think your instincts will tell you when or if it's time to leave.
For me, it's always been helpful to get a hold of as much information as possible, and talk as often as possible, and keep open and honest with myself etc. No one can really say how you're going to feel about this in a year for example, or whether your reactions now are simple programming or fear, or whether it's your gut feeling telling you to leave a situation that is damaging.
This is the whole excitement of it right?
You seem to be quite emotionally mature and your gf seems to dig you - two reasons I'd say you are quite some way off of needing to throw in the towel