This case has been blown way out of proportion. Just read the dissent in the Circuit court. There is no one Ms. Smith will not serve. But there are messages she will not express.
Religion has nothing to do with the matter legally. The state can't force a printer to print Nazi propaganda, and it can't force a website designer to create art that celebrates a rite she does not support, whatever her reason. Ms Smith does not need a reason to refuse to express a message, so long as she refuses to express that message on a non-discriminatory basis.
When I took the LSAT many years ago, there was a section where you had to select the narrowest rule that could be inferred from a given set of facts and judicial ruling about them. Suffice it to say that Mr. Sentell, and the rest of the Chicken Littles who think 303 Creative is a big deal, would have done very poorly on that part of the test. If 303 Creative is decided in Ms. Smith's favor, no one will be permitted to deny service to anyone, but no one will be forced to provide expressive services to anyone unless they would provide the same services, i.e., deliver the same explicit and implicit message (e.g., support for same-sex marriage, not just "marriage" generally), for others.
We should not conflate identity with belief. It may well be that virtually all gay people support same-sex marriage, but so, too do some straight people, perhaps a majority. The law would not allow Ms. Smith to create a website supporting a same-sex marriage for a straight customer (for his child, say), but not for a gay customer. That's not this case. Ms. Smith will not create a same-sex marriage website for anyone, gay or straight, and she will create non-controversial (by her lights) websites for anyone, gay or straight. It is the creation, not the customer, that the law cannot coerce.
The example of Christians having their own schools and universities is right on point. Presumably, a school cannot exclude a Jewish kid on the basis of his religion, but that school is permitted to have a curriculum based entirely on Christian beliefs. Anyone can buy Amy Grant's albums, but she is not obliged to write or sing anti-Christian songs.