Actually new thought: what if the Shadow is being controlled by the Blue Fairy, and the whole hourglass is an illusion made to set Malcolm/Peter Pan off on a quest to find the heart of the truest believer. Because perhaps later on, maybe in Oz, Henry is the only one who can defeat the Blue Fairy and she needs to find a way to very indirectly get rid of him?
I will accept anything that makes Sneaky Fairy Sneaky. It has been the one theory I refuse to give up since S1. I also think the BF might be sisters/allies of the Wicked Witch.