Basically, this has little to do with whether a snowflake is a religious image, and much to do with basic etiquette.
One is unlikely to go through life, in any belief system (religious, political, philosophical or moral), without being offered, in good will, a present that will conflict with it. The polite thing to do is to give thanks, and then dispose of the gift in a way that meets your own beliefs, and does not get back to the giver. Chastizing the giver for not recognizing your own stance (particularly when the giver was a 6 year old child), is well beyond the pale of polite behaviour.
If the family disapproves of snowflakes, they could have thrown it away. The literally holier-than-thou letter was unnecessary, and, I think, had less to do with any real pain on their behalf, and more about proclaiming just how noble they were in their own beliefs.