It depends on what the meaning of the words 'religious freedom' is...
Which entity do you trust more -- the Obama administration or the federal judiciary?
If you answered "Neither," I'd say you're right on the money.
To wit: Kenneth D. Whitehead, who served as a U.S. Assistant Secretary of Education during the Reagan administration, writes in Crisis Magazine online:
The recent decision by a federal court in Missouri to reject one of the lawsuits challenging the Department of Health and Human Services (HHS) 'Obamacare' mandate that requires near universal carrying of insurance plans that cover, gratis, contraception, sterilization, and abortion-inducing drugs raises troubling questions about how the courts generally are going to rule on the numerous other lawsuits currently filed against this misbegotten HHS mandate. Catholics and other opponents of the mandate believe it to be a grave violation of religious liberty, both under the First Amendment and under the Religious Freedom Restoration Act, but this recent Missouri decision judges it to be no violation at all on either count.
A for-profit, non-religious company, O'Brien's Industries Holdings (OIH), had sued claiming that complying with the mandate would violate owner Frank O'Brien's ability to operate the company in accordance with his religious convictions and practice; not complying would subject his company to ruinous fines that would have a crippling effect on the company's ability to survive economically.
Federal Judge Carol E. Jackson, however, rejected this lawsuit in its entirety, ruling that the company did not qualify for the (very narrow) exemption for some religious employers and holding that the mandate does not constitute the 'substantial burden' on anyone's religious freedom that the Religious Freedom Restoration Act specifies
With regard to the question of whether the mandate violates the First Amendment's guarantee of the free exercise of religion, Judge Jackson averred that the HHS regulation is an entirely 'neutral' instance of insuring women's access to 'healthcare,' and the First Amendment, in her view, does not exempt anybody from complying with neutral laws of general applicability. (Actually, in issuing the mandate, HHS simply defined by regulation, without any underlying legislative authority to do so, that the objectionable birth prevention procedures-contraception, sterilization, and abortifacients-somehow constitute 'healthcare.')....
Thus, we're now faced with a scenario in which a (secularist) federal judge can decide what constitutes religious freedom and what violates that "freedom." If a judge decides that mere belief in God is the only thing that should be permitted in regard to religious freedom, then he or she can rule accordingly. Sure, some may scoff at such a scenario right now, but, as Mr. Whitehead points out in his excellent analysis, our government is headed in that direction -- and it's downright scary.
The bottom line: Technically speaking, we don't have separation of church and state. We have subordination of church to state.