That occurred to me as well. But the idea that a person who is in a business cannot ever decline to do whatever a customer wants done is silly. It happens every day.
There's a big difference between "whatever a customer wants" and a customer going to a pharmacy to get a prescription filled.
If the customer expected to receive multiples of what the prescription offered that would be different. If the customer demanded the prescription be provided in a neon blue glittery bottle because they disliked bog standard orange plastic that would be different. Expecting a pharmacy to fill a prescription isn't exactly a far-out proposition though.
As someone else already commented, if the pharmacy really didn't want to offer that product they could always avoid stocking it. The nature of the morning after pill is such that telling a customer "we can get it in for you, it will be ready on Wednesday" isn't actually helpful to them, so it becomes much easier to refer them to a different pharmacy.
This pharmacist told the lady that another pharmacist would be coming on duty in a few hours and he would not likely have the same reservations, not being a pastor like the first one is. She decided to sue instead.
That's similar to the Colorado baker's case in which that man declined to decorate a wedding cake in a certain way but not to refuse to make and sell that customer any of a number of typical wedding cakes. He also took it upon himself to locate another baker who would decorate according to this customer's specifications. That was not acceptable because the intention was to bring charges, not to buy a cake.
Except it isn't really very similar at all. It's one thing for a private business to take a specific stance (e.g. the pharmacy deciding not to stock the morning after pill at all), where that stance is made clear. It's a different thing entirely when you can't tell whether you'll be served or not, and being served depends on who happens to be behind the counter at any given time.
Since you mentioned the Colorado baker it would seem more akin to a gay couple going to the baker, ordering their cake, being given a delivery date only to show up to collect their cake and find the person who happened to be working at the time refused to hand it over, saying they were welcome to return to collect it in a few hours when a different person should be in the shop.