I am very conflicted on this issue, but I think that the individual's (though really, this is not about individuals but about institutions like the Catholic Church) interest in religious freedom must prevail here. The reason for this is that the damage done to religious freedom is greater than the damage done to the people who must pay for their contraceptives.
Not to minimize the importance of money, but money is surely less important than religious values. A person who has to pay money that they otherwise would not have to pay is not harmed as much as a person who has to violate their religious beliefs. Therefore, I think that when you balance the competing interests in this conflict, religious liberty is the more important.