Unless they've changed the rules (not likely) du Lac specifically states that students are not allowed to create a disruption to a Notre Dame social or academic environment, and taking a knee at the game could technically be seen as creating such a disruption.
While I find it unlikely that the folks at Student Affairs would take any significant action against students who engage in such childish behavior, keep in mind, that if they're aiming to smack down a particular student that they may not like, then it's probably not a sound idea to give them any ammo with which they could shoot you. 50 hour community service sentences, etc., could easily be handed down at a whim.
First, and foremost, I don't support Student Affairs weaponizing such things. It's a petty move on their part, and to waste time engaging in such petty garbage reflects badly on the Golden Dome.
Still, you never know what the folks at Student Affairs may want to do. Maybe someone's looking to win a few brownie points with the folks higher up. Maybe that someone is looking to make a name for himself, or perhaps become the next Patty O'Hara... Is it really worth getting in trouble over a silly protest that could be carried out elsewhere?
Enjoy your lives as ND students. It's a blast of a time, and you're afforded an opportunity to study at the premier Catholic school in the world (my opinion, of course). Don't jeopardize that privilege.