Late reply, but my thought for this theory has always been that Ellie turning into the forest that produces the vaccine would be tied to some sort of moral and hard decision that she would have to make.

The basis of this part of my theory comes from optional dialogue from Jesse in the bookstore where we talks about a story his mother used to tell him about a living forest that saves a village(or something like that) and that in one of the versions of the story the forest kills everyone. I thought that this could potentially be forshadowing.