Allen is called "the Destroyer of time", what if this doesn't mean the Earl but someone else?
Miranda's innocence is time based, so it could be her to...

Also could Miranda be the heart?
Her innocence is the only non-offencive innocence in the story so far.
Allen's and Lenalee's innocence are the only innocence that has shown a form of free will, this happened after they met Miranda and came in contact with her unrestrained innocence (When it was still a clock).