Eliminating funding based on a small percentage of services that someone dislikes is like saying that no restaurant in the country can serve potatoes because you don't like french fries.
Our government has had a separation of church and state since the founding of our nation. Restricting funding for a government organization based on a religious belief crosses this line. Religious and personal morality crusades should not be involved in the running of our country or in medical services.
You can't deny women their basic rights about their bodies and pretend it's about religious freedom or in the name of a religious diety. Religious freedom doesn't mean that you can force others to live by your beliefs. Your viewpoints are yours alone. If you don't like birth control or other medical services, then you don't need to use them.