This is another piece in the discussion currently raging about the latitude members of a profession ought to have to follow conscience over the dictates of the profession.
Professions are communities of a sort. What unites them is that the members of that community are taking on a certain set of shared values.
This does not mean all members of a given profession are unanimous about all their values. A profession does not assimilate its members like the Borg. Indeed, there's something to be said for a professional community that reflects a diversity of values and perspectives -- it gives people in that profession the opportunity to try to see things through someone else's eyes. This needn't make you change your stance on things, but it helps remind you that your stance isn't the only one that a reasonable person (at least, a person reasonable enough to be a member of your profession) might hold.
The big question, as has become clear in this discussion, is what ought to happen when the values of an individual within a given profession are in tension with the "shared values" of the community -- where the "shared values" I have in minds are the ones explicitly specified in the professional code governing that profession. Such a code can be like a mission statement for the profession: this is what we stand for. But what about the members of the profession who don't endorse all those values?
A dissenting member has the option of leaving the profession over the disagreement. Or, the dissenting member can stay in the professional community and try to work it out, either figuring out how to embrace the value in question or working to persuade the professional community to change that value. I don't think pretending to your professional peers that you embrace the value in question -- either going through the motions of letting it guide your professional actions while doing so eats away at you, or skulking around and doing the opposite of what a professional guided by that value would do -- is a good idea. Both options require being dishonest with your peers in the profession, and the latter can also involve being dishonest toward the people your profession serves. (For example, the professional code says you'll do X when called upon to do so, but you won't. Yet, given that you're a part of the profession committed to doing X, the client has every reason to believe that you'll do X.)
If the dissenting member of the profession isn't committed to trying to work through the disagreement, she isn't fully committed to the community.
None of this is to say that professional codes always articulate sets of values that are internally consistent, or that there might not be good reasons to change those professional codes from time to time.* Some values may be integral to what the profession is all about, while others may be dispensible. Members of a profession who engage in dialogue to identify commitments of the community that are dispensible can be good for the community. Imagine a professional code for scientists that specified that members of the profession must be white, male, and heterosexual. Surely it would be a good thing for members of the scientific profession to pipe up and say that this requirement of the profession is not in any way a requirement for the overarching goal of science (i.e., applying a particular approach to making sense of phenomena). If all the members of the profession who thought this was a stupid value to enshrine in the professional code simply left the community, how would the profession ever move past this unfortunate requirement?
If the conflict is about a value integral to what the profession is about, however, there may not be room for negotiation. The member dissenting from that value will have to make the case to the community that the disputed value really can be excised or changed without totally changing the nature of that profession. And, if the community is not persuaded, the dissenter has to expect that she won't be regarded as a real member of the community any more, no matter how much she feels the other values shared by that professional community to be her own.
It's a good thing for members of a profession to stay in dialogue about the commitments they share, and especially about the commitments that are essential to the aims of the profession. However, without a core of shared values uniting members of a profession, there's no longer a community. To the extent that being a professional involves having to answer to one's professional community, certain kinds of dissent are deal-breakers.
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*It's also worth noting that belonging to a profession that has a professional code of ethics does not guarantee that you know all of what is articulated in that code -- or even that you know that your profession has such a code. (Google your professional organization and "code" and see what you find.)
In fact, in a Kuhnian sense, the vitality of the scientific endeavor depends on challenges to the body of "normal science" -- I would think that this winnowing process applies to the ethical practice of a science as much as the accepted content of that science. If nothing else, these challenges force us to make explicit the criteria for legitimate content and legitimate practice that we've been holding implicitly. But, in the meantime, it's messy and people suffer the consequences of our confusion... I'm glad that you're addressing the messiness.