Should conscientious public servants resign when their job conflicts with their religious principles?

There's been a lot of talk about Martha Coakley's blunt statement that those who want to adhere to religious scruples against abortion and birth control "probably shouldn't work in an emergency room." I put up a long post about it earlier today, and I'm not going to repeat myself here. The point of this post is to compare Coakley's statement to something John F. Kennedy said about the conflict between public service and religion back when he was running for President and questions were raised about his Catholic religion:

I believe in an America where the separation of church and state is absolute; where no Catholic prelate would tell the President -- should he be Catholic -- how to act, and no Protestant minister would tell his parishioners for whom to vote; where no church or church school is granted any public funds or political preference, and where no man is denied public office merely because his religion differs from the President who might appoint him, or the people who might elect him.

I believe in an America that is officially neither Catholic, Protestant nor Jewish; where no public official either requests or accept instructions on public policy from the Pope, the National Council of Churches or any other ecclesiastical source; where no religious body seeks to impose its will directly or indirectly upon the general populace or the public acts of its officials, and where religious liberty is so indivisible that an act against one church is treated as an act against all....

I do not speak for my church on public matters; and the church does not speak for me. Whatever issue may come before me as President, if I should be elected, on birth control, divorce, censorship, gambling or any other subject, I will make my decision in accordance with these views -- in accordance with what my conscience tells me to be in the national interest, and without regard to outside religious pressure or dictates. And no power or threat of punishment could cause me to decide otherwise.

But if the time should ever come -- and I do not concede any conflict to be remotely possible -- when my office would require me to either violate my conscience or violate the national interest, then I would resign the office; and I hope any conscientious public servant would do likewise....

So, according to JFK, the President is supposed to make decisions "in the national interest, and without regard to outside religious pressure or dictates," and if, because of religion, he can't do that, he should resign. Kennedy doesn't limit his resignation imperative to the presidency. Such a limit would make sense, as there is only one President, and the nation's reliance on his judgment and action is extreme and unique. Kennedy applies his imperative to "any ... public servant." If you take a public service job, that is, then what you owe the public is service according to the public interest "without regard to outside religious pressure or dictates."

Is an emergency room employee a "public servant" to whom Kennedy's resignation imperative should apply? That job is not an "office." You aren't elected to it, but you are, by taking that job, holding yourself out as ready to perform the duties associated with it. Is it right for you to take exemptions for your own sake at the expense of the public you were hired to serve? Maybe your need for an exemption from part of the job is a conflict between personal and public interests that should lead you — if you are conscientious — to resign.

I think Kennedy's imperative becomes too harsh at this point. For one thing, there is a long tradition of religious health care workers serving the public. There is a special energy and altruism that comes from religion that we shouldn't want to lose, even as government money and mandates reach deeply into health care. Nor should we want to alienate and marginalize citizens who belong in the mainstream of American life. Even those of us who believe in the importance and the right of access to abortions and birth control should want to find ways not to brutalize these workers. We shouldn't want to demand that they give up their livelihood unless they are willing to commit what they believe is murder. I hardly think John Kennedy meant for his vision of the separation of church and state to include something so perverse.