Going through someone very similar as well, except it's a divorce. One thing I'll tell you is first priority is your child. You seem to be doing fine with that, I just wanted to make that clear.
Now dealing with your ex... my ex wife says she loves me every time we see each other. However much like yours, she says she "can't take the chance."
Unfortunately, the types of separation we are experiencing, are not ones easily fixable. I hate to say it, but the best thing to do, may be to give her the space she wants, and try and show what a good father, and overall person you can be. Work on making yourself be the best person you can be.
there are 10 types of people in this world. Those who understand binary, and those who don't.