Except that the Church isn't in the Medical Business for the good of humanity.
They are in the medical business to make money. And they get a lot of special tax breaks to do so, which I personally have no problem with.
But here's the thing, they should follow the same fair labor practices everyone else has to follow when conducting business... and that means providing proper coverage for their employees.
Birth control is cheap. The Catholic entities do provide proper coverage- They are free, by the their first amendment rights, to not provide a product that contradicts their religious beliefs- No one in forcing said employee to work for such an organization.
My problem is, that shouldn't be their call. Proper medical treatment should be determined by the doctor and the patient, not government, churches, insurance companies or employers.
Unless you want to do the breathtakingly rational thing and have single payer for the whole country...
Let's follow your rationale to its logical conclusion. No planned parenthood counselor should give abortion counseling to women. It shouldn't be their call. It should be determined by the doctor and the patient without third party counselors.