Take into account that although the Hobby Lobby v Sebelius case sprung up questions between religion and government, their arguments weren't even valid to begin with. Their first argument was that although the Affordable Care Act permitted them to choose not to provide insurance, they were being taxed " applied financial burden" and doing so harming the company. That was a joke, their numbers showed that tax was way less than what it could cost to provide each employee with full medical coverage as quoted by Justice Kagan, "you can't call something a financial burden when it in no way harms the individual(company)." Also, the Affordable Care Act also stated that should an employer deny an employee coverage, they would have to give the employee a sufficient amount of pay that would allow the individual to seek outside coverage. And even then, their numbers showed that that option was cheaper than choosing to give each employee coverage.
Second, they tried pulling the Free Exercise Clause of the First Amendment which was automatically shut down by Justice Ginsburg. The Affordable Care Act does not address that the tax applied was a consequence of the decision to not give coverage to an individual because of their religious affiliations or decisions. They were given well detailed options that either way was the smarter choice than choosing to bring their "useless" complaint to the floor.
Now I'm not saying that the question between Religion and Politics is answered through the Affordable Care act for this case or any situation. Our government contradicts itself with the Religion Clause by opening sessions with prayers and using the Holy Bible in Courts. But the argument the that Affordable Care Act hinders one's religious decision is just not valid.