The establishment clause says we have freedom of religion. Not freedom from religion. The difference between the bakers is that their freedom of religion was being usurped by someone else's sexual ideology that conflicts with their religious spiritual belief and forcing them to support a sexual ideology that their faith considers harmful.
The Red Hen is a restaurant has a menu. Sara was not asking them to create something not on the menu. She came in to order from what they serve. She was not there to force them to cook food they did not want to make.
Kicking anyone out because of who they work for, or their political affiliation is not the same. Nothing of this interfered with the red hen to cook the same meal they would serve to the people sitting next to Sara, to Sara herself. She was not in their voicing her political beliefs, or her ideology. She was just a patron trying to order off their menu.
These two cases don't compare in the slightest. A Muslim restaurant owner could also deny to make bacon for a patron. And rightly so because it goes against his/her religious belief. This case would compare to the bakers and the Muslim would win also.
However the Muslim could not deny service because someone is a Democrat or worked for a Dem. This goes the same for Republican, etc etc.