If Whedon is atheist as suggested that's a pretty good reason to not represent Christmas in his work even in commercial form.
Let's say an English class is assigned an essay requiring the students to describe the origin of a holiday of their choosing. A Jewish student is probably not going to chose to write about Christmas unless they want to explore their beliefs and likewise a Catholic student won't choose to write about Hanukkah.
To represent/practice a holiday in any way is an allegiance of it's origin even if you choose to ignore it and Whedon probably didn't want his beliefs questioned or solicited by portraying something that he's supposed to be against in his work.
Since I'm a Cangel fan would you question me for not ever writing a Bangel fanfiction?
Well..we do know Santa Claus exists! Courtesy of Anya who knows the guy.
Actually she specifically uses the name 'Father Christmas' who in origin is a different figure from Santa Claus. Father Christmas originated in English Pagan lore as a 'yule tide visitor' dressed in green who was the embodiment of the winter solstice and was firstly known as Father Winter or Father Frost. He is believed to be one of multiple forms taken by the god, Odin and it was thought that by welcoming him into one's home on December 6th and offering him food and drink a less harsh winter would be granted as reward.
The Ghost of Christmas Past character in Dickens' 'A Christmas Carol' as illustrated by John Leech was designed around this Father Christmas figure.
It wasn't until the 1870's that America begun to associate the name with the Santa Clause figure. Coca-Cola was actually a large part of this, I believe it was them who'd changed his outfit from green to red.
http://www.timetravel-britain.com/articles/christmas/santa.shtml
http://www.christmasarchives.com/england.html
Though considering if memory serves that Anya had a negative notion of the figure she spoke of it's more likely she was referring incorrectly to Krampus. Krampus is Santa's dark counterpart. While Santa rewarded the well behaved children with gifts Krampus was said to be the yule-tide visitor of the naughty children who would leave them coal, beat them and in some versions take them to hell shackled and stuffed in a sack.
http://thefairytaletraveler.com/2013/12/21/the-dark-side-of-christmas-the-legend-of-krampus/
http://www.halloweenartists.com/krampus_event.htm
http://www.krampus.com/who-is-krampus.php