Of course, our campaign circus 2016 has Trump positioning himself as the champion of Christianity, even though two major conservative news outlets have denounced his positions on religious freedom (National Review and American Conservative). Meanwhile Hilary Clinton, whose husband Bill has an actual track record of controversial advocacy for a Religious Freedom Restoration Act (RFRA) last time it was hot (1993, related to Native American traditions, struck down by the Supreme Court in 1997), has bashed the latest round of RFRA proposals, designed mostly to protect conservative Christians from laws banning discrimination on the basis of sexual orientation.
In recent SCOTUS history, justices nationalized gay marriage to every state in Obergefell, and in Burwell v. Hobby Lobby, they ruled that corporations owned by religious people (counting as religious people themselves) cannot be required to violate their consciences and provide contraceptive health care to employees. According to Gutterman and Murphy, the Hobby Lobby case is dangerous because it allows the possibility for any corporation to violate all sorts of federal labor regulations. The authors don't discuss this, but this case has the power to set such precedent because of a previous case.
Mid-century, there were many important Supreme Court cases, but in my mind one of the most important was U.S. v. Seeger (1965), which expanded Conscientious Objection status from traditionally religious pacifists to anyone whose "conscience... would give no rest or peace" if they participated in war. According to Phillip Hammond, this case represented a major shift in interpretation. In other words, all sorts of deeply held convictions now "counted" as inviolable under the "free exercise" protection of the First Amendment. Personal "conscience" was the equivalent of "religion."
Thus, even granting that the Affordable Care Act represents government over-reach, Seeger + Hobby Lobby does in fact combine to open the way for all sorts of corporate labor abuses. If a random individual has a strong enough conviction about something (not hiring women, not paying minimum wage, not paying taxes that support x, y or z) they may have a case. The Libertarian end of the political spectrum might think this is all "in bounds" and the market will sort it out. On the other hand, lower courts in Oregon, Texas and Colorado have not upheld the cases of Christian cake bakers who refused to bake cakes for gay or lesbian weddings, but SCOTUS has not had to deal with any such case so far.
How various POTUS and SCOTUS choices will deal with our current milieu over time is hard to tell. I'm fairly confident that politicians will be politicians. George Washington, for all his irenic statements and respect for religion's role in society still valued "the interests of the nation" above "the conscientious scruples" of citizens and expected the citizens to give government "on all occasions their effectual support" (letters to Quakers and Jews respectively, qtd. in Gutterman and Murphy, 1). In other words, don't expect them to do anything that isn't in their own interests.