Religious liberties are not absolute.   If consciences are to be burdened by a generally applicable federal law that advances a compelling government interest, the Religious Freedom Restoration Act requires that this be done in the least restrictive way possible. It's not sufficient to maintain that such a burden only amounts to a remote material cooperation (e.g. opt-out accommodation); it's necessary to establish that no other way would be as practicable & effective. 

The question thus turns on the government showing that alternate distribution channels are infeasible. Since the Affordable Care Act model revolves around employment-based health insurance, the goverment has argued that requiring other distribution alternatives would upend that model, which the law, itself, presupposed as the most feasible means. That presupposition was already well founded & well grounded, as that model's feasibility had been empirically established and long-practiced. 

The need must be met somehow!