Conscience Clauses and Institutional Autonomy

My post on conscience clauses (below) prompted this response from my colleague Susan Stabile:

I read with interest both Rob’s comment and the CNN report on conscience clauses in the health care industry. I have taken the position that Catholic employers should not be forced to provide contraception coverage for their employees. (I published an essay on this issue in the Spring 2004 issue of The Catholic Lawyer and have recently completed a longer treatment of the subject.) However, as I read some of the examples in the CNN article and Rob’s comments about moral responsibility of professionals, I have some misgivings. It seems to me that it is one thing to say that a Catholic organization should not be forced to violate its (institutional) conscience by paying for its employees to do something the organization believes to be a moral wrong. I’m less comfortable saying that an individual Catholic employee opposed to birth control who works for a profit (nonreligious) pharmacy is entitled, based on his/her individual beliefs, to not provide a service the employer makes available to its customers. What I’m struggling with is where one draws the line (if at all) and would be interested in hearing other people’s thoughts.

I think Susan raises a good point. Normally I'm concerned with our society's elevation of individual autonomy over associational autonomy. Are conscience clauses part of that trend? If we defend the right of Catholic organizations to carve out a pro-life identity for themselves, should we be more hesistant before requiring other organizations to sacrifice their own institutional priorities to the individual consciences of their employees?

Rob