Supporters of the HHS decision not to broaden the religious exemption (or who think the objections to it are overwrought) for the directive to include coverage for contraception in employee health benefits point to the absurdity of an organization as large and diverse as the Catholic Church having a "conscience." The proper unit for considering the right of conscience is the individual, and that, from this perspective, it is the Church that is imposing its morality on the conscience of its employees, the vast majority of whom do not share the Church's opposition to contraception, and that through the mandate, the administration is freeing them from this imposition.
They have a point, if one thinks that the most important things is to preserve the conscience rights of the individual.
But I'm not sure that's the crucial thing.
I'm reminded of an article several years ago from Emily Bazelon several years ago about doing a book swap instead of birthday presents for her childrens' birthdays that I commented on. While I wasn't, and am not, a fan of this particular innovation, I saluted (and continue to salute) parents taking a stand against the rampant consumerism surrounding birthdays and other holidays.
Of course, this can be seen as the parents dictating to the children how their birthdays will be celebrated, and an individualist might claim that the child should make that determination for his own birthday, and the parents have no right to do so.
But notice where this thinking will lead us -- the individual child will tend to conform to the mainstream of society -- he wants a party with presents just like every other kid! And this status quo of consumerism will remain unchallenged. When we make the unit of conscience rights the individual rather than families or other organizations, what we are really doing is privileging the status quo, because an individual is less likely to effectively resist the mainstream than an organization.
History demonstrates that the US mainstream has been terribly wrong on many issues, and thus it's likely we're terribly wrong about something now. Most will scoff that our embrace of contraception is one of those things, but I think there's a non-zero chance that it is.
But if it is, or if some other aspect of mainstream culture is a great mistake, we will need alternatives to show us a better way. And leaving it to individuals isn't likely to get us there, because individuals are easier to sweep up in the mainstream than institutions like churches and families are.
I'm not sure "conscience" is the correct term to capture this -- perhaps institutional diversity or institutional pluralism? But we need space for institutions to dissent from the mainstream of cultural practices. The Administration's action closes this off, and that's a bad thing.