Yes I completely agree, and that's why I think she's is gonna be in trouble or something. I don't think she's is gonna die, but maybe hurt or do something, like kill somebody.
I feel like they need something more than just the hunt for the last episode, and we already know he would go the extra miles for John, Mrs Hudson and Lestrade.
We never really found out what she did to help Sherlock, we only know that she matters because he said so, and that she helped him in someway.
She is very important, but her role has been very small the last two episodes, a façade relationship, a " let's go sleuthing together joh..molly" throw the girl a bone.
But maybe I'm completely of, I am not familiar with the writing style of Gattis and Moffat besides this show, I just can't shake the feeling they have a surprise up their sleaves and where they want to go with Molly.