"...and does not provide charitable services primarily to Catholics."
I assume you are not a Catholic if you think that a Catholic charity should provide charitable services primarily to Catholics.
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.