couple of henry's remarks:

Crispin makes a good point that the consequences are usually worse when people violate their consciences than when they abide by them. But his conclusion, that we should ALWAYS respect their decisions to abide by their consciences, does not follow. There is no reason that we cannot decide on a case-by-case basis.

Let's keep in mind that we are discussing only the right of an employee to keep his job after refusing to perform one or more of the duties of the job. We are not discussing the right of an employee to quit his job. We should respect his right to quit for any reason; this includes the right of a soldier to refuse to fight a war that he considers immoral.

first off, resting the question on a case-by-case evaluation vitiates the entire notion of individual conscience. or: it sets up the evaluator as the arbiter of individual conscience. follow your conscience, except where we disagree. by default, it sets up the institution as the arbiter. e.g. of course we respect individual conscience, but this is the final solution we're talking about, the only hope for the future of mankind. and second, one should reduce barriers to conscientious action as much as possible: one important dimension of moral evaluation for any institution is the extent to which it can do this. requiring more or less heroic action (e.g. quitting my job, thus fucking up my family etc), forcing me to flee to canada etc: these are essentially totalitarian contexts. of course, it's a matter of degree, and if, for example, a pharmacist converted to christian science and declared she wouldn't dispense any medications, but wanted to keep her job, that wouldn't make any sense. on the other hand in a case in which we're talking about one limited function of the job, and where the person regards the matter as raising absolutely fundamental religious/moral questions, the institution should respect individual conscience. the extent to which it can is one extent to which it is relatively decent or relatively dangerous, compatible with freedom or totalitarian.