I disagree. In very many situations, as you describe it, stockings are for family members.
To deny SIL and her new husband a stocking is to say, "you don't count if you don't show up." I can't think of anything less appropriate to the sentiment of the holiday.
You didn't say whose home the gathering is in, and under which family auspices this has been arranged. But they are being created by the participants, and not by the hostess. Therefore the *group* gets to decide how they will be handled. At least one member of the group has already declared that she sees them as a "family togetherness" thing and expects all family to be included every year, period, no matter where they end up celebrating.
Your approach to the stockings treats them as sort of a party favor. That's really unappealing to me at Christmas and among family. Especially when they are being *created* by all the participants, and not by the hostess.
To me, this is even *more* than a one-time, "We had extra food, and you helped prepare it, so here's a meal for you." Gifts are ways we express our love for one another. To treat them like a party favor is really hurtful.
Were I SIL's mom, that's not a message I'd want to sent to my new son-in-law--I'd want him to feel that he's valued, etc., so that maybe he'll have warm feelings toward us and want to include us in their lives.
Were I SIL's sibling (your partner?), I wouldn't want to send that message to my sister: "If you're not here, I'm not doing anything fun for you, and I don't care about your new husband either." Way to make sure they *never* show up for Christmas again. They sure don't have to, I'm sure his family would love to have them for all the holidays!
Of course they'll miss out on the fun of opening stockings right that day. And the rest of us will miss out on seeing them react to what we've given them. But that's a small price to pay for treating them like members of the family, even if they are absent. For sending the message (which is what gifts are intended to do) "I love you."
And I'll confess that if one of my daughters-in-law expressed the sentiments in the OP, I'd look at her differently for a long time!
And I found this sort of offensive:
This Christmas my SO's sister(SIL) got married. She has decided to spend Christmas with her new family. She lives the same distance away that she has for the past 10 years.
if SIL was still single but had to be away from the gathering for reasons beyond her control
So because she has gotten married, now somehow she's getting "dinged" because she is considering her husband's wishes and spending time with his family? It sounds as though you think this is some unimportant whim--as if you think she said, "Oh, I don't want to come to your house this year, I have somewhere better to go." As if she is rejecting you ("...her new family...") because she now has competing demands on her time at family celebrations.
I would classify "have to spend Christmas at her spouse's family's place" **as** a reason beyond her control. What is her other choice? To be disrespectful to her new husband by refusing to consider it?