Ah ha! That actually makes a lot more sense. I had already read a synopsis going into the movie and kind of carried that assumption with me.
IMDB Summary: Spanning over one thousand years, and three parallel stories, The Fountain is a story of love, death, spirituality, and the fragility of our existence in this world.
So I'd kind of just taken it for granted that each of the time lines was an actual occurrence.
Now that you guys mention it though- the inquisitor could symbolize her cancer, the tree of life is her cure, etc. I was wondering how the tree of life was supposed to stop the inquisitor, but in light of the symbolic angle, well of course it makes sense.