I remembered how I thought she had a confused conception of meta-ethics and that she often seemed skeptical of reductionism, which in retrospect should have been a major red flag for purported atheists.

From my view, reductionism is the basic question. If someone is right on evolution but wrong on reductionism, that really doesn't buy them much- and I would wonder how deeply they grasp evolution.

As to how to navigate this: suppose that she has a psychological need to profess a belief in some sort of deity, such that she could not fully thrive without professing that belief. Would you want her to be an atheist then? How can you tell if she has that need or not?