The story that Target allows its pharmacists to refuse to dispense emergency contraception on religious grounds checks out. It's not surprising, given that several states may well pass legislation to extend this supposed right to all pharmacists. This seems worthy of no longer shopping at Target, or rather contacting Target to tell them they will not be receiving my business, while neglecting to mention that they didn't in the first place. You might consider doing the same.
It's clear to me that pharmacists do not, and should not, have the right to refuse to fill prescriptions on religious grounds. The reason religious anti-discrimination has nothing to do with it is that the pharmacists aren't being discriminated on the basis of their religion, rather, they're not being allowed to hold a job while acting on beliefs that prevent them from meeting the requirements of the job. So far, so good.
Here's a test case that shows things to be a little more complicated. The job description of a doctor(1) is to provide patients with medical care necessary to alleviate or prevent illness and improve the quality of life, while also making the patients feel comfortable and inspiring confidence. Now transition to the south in 1960 or 1950, and imagine the following line of argument "Refusing to hire Black doctors is not discrimination on the basis of their race, it's just refusing to hire people who are not capable of discharging the function of their job. If we hire Black doctors, patients will be uncomfortable, and won't trust that their doctors can help them." I take it this argument is wrong, whereas the first was correct. But it's also obvious that the premise about how patients would react was correct.
What this shows is that we ought to think very carefully about the reasons underlying what constitutes discrimination (and the limits of state and corporate power in general). As liberals, broadly defined, we've usually got the right intuitions, but we don't know exactly why we have them. Belle did a good job of exhibiting this by posting one of the best arguments against same sex marriage (at least outside of queer theory, if you give those arguments any credence) and then quickly taking it back, but leaving a skeleton of it behind. Though I'm not sure Belle draws this moral, what her exercise shows is that it's worth thinking about whether you aren't just another "handwaving Burkean conservative" who just happens to believe in gay marriage and reproductive rights.
It's times like these when I want to do ethics and political philosophy. *sigh*
(1) Was going to say waiter, focusing on the comfort of the diners, but then I realized that most southerners were probably perfectly comfortable being waited on by Blacks.