Really sorry sbout your loss OP.
It wasn't good timing to send presents, the way it all reads very much depends on your relationship the rest of the year.
It sounds as if inlaws and you have the same Santa tradition:
- Santa fills the stocking left out by the child, these come from Santa and delivered by him on Christmas Eve.
- All other presents come from the person who brought them.
- There is no "Santa left me these at my house for you" tradition. Or Aunt Matilda brought these, posted them to Santa, who then delivered them back to be put in the stocking?
This is how your husband experienced Christmas, this is how you want Christmas to be for your children, you have told MIL this. Your MIL has decided to randomly put a filled stocking together with a note about to Nanny's Special Boy from Santa in a situation when you can't deal with it 
Maybe she is being helpful and thinking about you and her son not having the energy to do it all this year. Or maybe she is tying to get in there first and carry on being Santa. Maybe a bit of a mixture. Only you and your husband will have a clue about that
To cover all basis is it possible to thank her for the filled stocking and advent THIS year. That you appreciate her consideration that you and her son maybe wouldn't have time THIS year, due to the funeral. Crack a joke that the baby will have sooo many presents from Santa. Then drop it for next year and see what she does.
What you do with the advent and stocking very much depends on how much you see them over the festive period. If it's a beautiful calendar and you see them regularly then it could be proudly hung up every year, mil could be tasked with filling it every year if she so desires. If they hardly visit then they will have no idea! Then next year if she tries on the stocking thing again, despite knowing the norm in your house, then you will have to do a swift reminder that they will be presented as from Grannie. She can knock heself out with presents and fun gifts but they are not from Santa.
If I've got it all wrong and the reality is that ; her own grandparents did a stocking to her from Santa, along with ones from parents, Aunt Matilda, Doug the family Dog, the magical Cat collects them all, puts them on the Polar Express, for the elves to collect at Bonkers Station, who put a spell on them to send Santa, who then delivers them back to random relatives to give on random (he really needs a better address book and map), then ignore most of my post
and try to have a nice chat with her about it.