During the early section of Episode 5 when the player is on the roof Lee, of the player chooses to look it, will notate some blood that can be found on the roof which runs off the side of the hospital and he comments that he or she got injured.This:
http://www.youtube.com/watch?annotat...&v=9s7YhwDxWvU should bring some light as to what I am talking about, go to 7:45.
So I wonder as to whether or not this comment on the blood hint at the death of Molly as there is the possibility that she may have been injured and perhaps she fell to her death from the Hospital roof following an incident regarding her travelling by the high ground. I am not saying that this is the case, but Molly's absence does make me entertain the idea.