This should be entirely up to the individuals involved. It should be between an employer and an employee to negotiate the terms of that employment, and of compensation therefore, and if that compensation is to involve health insurance, then it should be between the employee, the employer, and the health insurance provider to negotiate the details of what that insurance will or will not cover.
There is nowhere in this transaction that government has any business being involved.
We have here a conflict that exists only because government has stuck its nose where it has no business sticking it. Without government's completely-unwarranted interference, there would be no conflict between an employee's “right” to “free” birth control, and an employer's right not to pay for what that employer considers to be immoral.