I agree with The Dude. The law requires the company to provide a health insurance plan and among other things, birth control is an item that must be covered to fit the criteria. Employees at this company have access to this health insurance plan and that's the end of it between the employer and employees as far as the employees health care decisions are concerned. It's then between the patient and doctor if some employees are using their coverage to get birth control. Or maybe none of the employees will use the coverage for birth control. Either way, as religious concerns go, the employer hasn't been violated in any way.
Insurance is a risk pool and birth control is a very commonly prescribed medicine. It isn't really about whether or not the employer believes in birth control personally or religiously. They just have to provide adequate coverage for their employees, and the employer is going to have to provide it whether or not anyone at the company is using birth control because that's how insurance works.