Sorry for not being able to (in my short week of fandom) exhaustively study all theories regarding Molly. I will try to catch up. 
However, a few things occurred to me:
1) When Molly says, "I don't count," Sherlock looks surprised. He could feel a bit of guilt, but he could also be processing the possibility of her usefulness. Given that he's recognizing his friends are his weakness against Moriarty. Molly can be very useful to him if Moriarty doesn't process that she matters. Ah, here is a potential ally and tool.
2) On the roof, Sherlock gives good space between his speaking, and waits for a response from Moriarty between names.
S: John?
M: Everyone.
S: Mrs. Hudson
M: Everyone.
S: Lestrade? (Pause)
M: Three gunmen, three bullets.
Moriarty CONFIRMS for Sherlock that the number is three. Had Moriarty said "Everyone" after Lestrade, I suspect that Sherlock might have named Molly to see if she is #4.
There were three IOU signs. Sherlock has deduced John, Mrs. Hudson, and Lestrade (based on the locations of the graffiti). Molly says she doesn't count, and Sherlock is hoping that she has flown under Moriarty's radar as a friend. On the roof, he speaks in just such a way to confirm that fact - there are only three.
Molly can help him, and he can maybe pull off the jump without M's knowing it's faked.
That's my theory. 
Fillyjonk
Check my Tumblr for a musical tribute to Sherlock's devotion during series 3.
http://imtooticky.tumblr.com