That was just one of the factors used in the San Francisco case to determine that Catholic Charities is not a religious organization. Even though Catholics are expected to be charitable to others regardless of their religion, it should definitely be done in the context of Catholic doctrine and Catholic moral teachings. A person who is treated in a Catholic hospital should know that he/she is in a Catholic hospital, for example. This means a crucifix in every patient's room, constant presence of clergy and people from Catholic orders, etc.
First of all, I volunteered hundereds of hours for a Catholic children's hospital in St. Louis a few years ago. They have crucifixes in every patient room and a strong presence of clergy.
That hospital is not alone. (It is an SSM hospital, for those interested.) The majority of the hospitals in that area are Catholic and all of them live up to their name, serving "in the context of Catholic doctrine and Catholic moral teachings."
Secondly, to everyone who is quick to chastize Catholic Charities in general, I would like to share a personal story. My father is a (not-so-)small business owner, and several years ago, Catholic Charities contacted him to ask if he would offer jobs to Albanian and Iraqi refugees who were in the process of becoming citizens. My father accepted and, since then, has maintained a relationship with the extended families of those original, legal immigrants. This is just one small example, but I think it hits right at the core of what Catholic Charities is about. They facilitated a connection between a Catholic employer and immigrants looking to become true Americans, as my great-grandparents and grandparents did not so long ago.