Canon-wise, Lily's the emotional link between Harry and Snape, and Snape's fate was pretty much foreordained by his guilt at her death. It made sense to me to give her the power to choose what kind of fate he would ultimately have, assuming it hung in the balance. The question was whether or not she would forgive him.
And yes, I decided to leave baby Tom's status a bit of a mystery, except insofar as Lily's obviously come to care for him.