There is no reason that the option for birth control should be removed in health insurance where employers have a moral issue. The employers should employ a "don't ask, don't tell," strategy because the freedom that we need to protect here is the option to choose birth control or not.
Birth control is a massive cost reduction in terms of health care delivery and women have the right to control when and where they get pregnant. If we can reduce costs and increase human rights then there should be no reason whatsoever for a company to be able to stop such progress.
I do think that all health plans should include birth control. Why wouldn't they. You know what's more expensive than birth control? A pregnancy; by a lot. And not all mothers are prepared to be, well, mothers. So of course this is good to have included in Affordable Care Act.
I think its going to have the employers spend enough for the care of their employees, birth control is something that they should buy themselves. Its not that expensive and they are grown adults, if they want children they can have them, if they don't, well they should have bought a contraceptive.