While "religious freedoms" need to be respected (IMhO), so do "laws of the land". This clerk might well be honestly "troubled" and even "fearful"; that if she does something which she believes will jeopardize her own safety and well-being, she might then be "untrue to herself", and that is a very powerful sentiment or emotion to deal with, as we know.
Additionally, just because the laws change does not mean everybody HAS TO believe they are "justifiable" or "right" or otherwise "appropriate". We all still do have a right to our own beliefs, even if they don't agree with laws of the land, don't we?
So, the REAL question becomes one of discerning what is actually more important? That a person be "forced" to behave in ways which oppose their personal belief systems, or that a person be "denied" the guaranteed (Constitutional) right to practice their chosen religion "freely", in spite of their "job description" interfering with that?
Another scenario is playing out for a Muslim flight attendant who refused to serve alcohol on a particular ExpressJet™ flight. Apparently, there was some kind of 'agreement' with the company that allowed for her to have another flight attendant do that part of the job when asked by passengers for alcohol; but apparently another employee made a complaint about that, and subsequent 'refusals' put the flight attendant in some hot water (see http://news.yahoo.com/muslim-flight-attendant-suspended-not-serving-alcohol-171403654.html).
These are likely the "tip of the iceberg", and we'll probably see much more of the same, going forward. Not sure how it will all unfold, but it is undoubtedly one of those things which will keep our attention for some time, I'm thinking.