The argument that employers such as Hobby Lobby have a right to refuse to pay for birth control seems nonsensical on its face.
My employer pays for everything* I buy. They pay my rent, my food, my car, my beer, my movie tickets. All of this money comes from my paycheck. Traditionally, we hold that although my employer pays for everything I buy, they have no standing whatsoever to tell me how to spend it. We could, of course, make a different social decision about that, but if a principle of law is to keep things consistent, then the obvious answer is that the employer is paying employees in money, and employers cannot dictate what employees do with that money, whether the money is paid directly to the employees or passed through directly as premiums to an insurance company.
*Or would if I still worked a straight job.
Just that companies are mandated to buy insurance does not change anything. Companies have a lot of coercive mandates regarding my paycheck. They have to pay me the minimum wage, they have to pay me for all my time, they have to pay me on time, they have to pay social security taxes (mine and theirs) and unemployment insurance premiums, etc.
The whole point of paying employees in money instead of in kind is precisely to place the decision about what to consume in the hands of the employees. If we are consistent on the principle of payment in money, then we either say that employers have no say on how employees spend their pay, or employers have say over everything employees buy with their pay.
Of course, the consistency the Supreme Court is actually employing is that conservative employers have say over how female employees manage their sexuality. Women (especially women workers) are, of course, inferior, and women's sexuality is evil (unless they're having sex to pop out Republican babies and no orgasms please). It is of the highest social necessity that someone regulate women's sexuality; if we let government do it, we might end up with something (ugh!) democratic. It's much better to place this regulation in the hands of corporations; the owners of land and capital have been explicitly and intentionally insulated from democracy since the founding of the republic.