Religious liberty supporters outside the Supreme Court building in Washington D.C., June 26, 2015. (Addie Mena/CNA)

WASHINGTON, D.C. (CNA/EWTN News) - Friday's Supreme Court ruling against the traditional understanding of marriage may pose huge obstacles to the free exercise of religion and conscience across the US, the nation's bishops have said in response to the decision.

"The free exercise of religion means that we have a right not only to debate it openly in the public square, but to operate our ministries and to live our lives in accordance to the truth about marriage without violence, or being penalized, or losing our tax exemption, or losing our ability to serve the common good through our social services and through education," Archbishop William Lori of Baltimore, chair of the U.S. bishops conference's Ad Hoc Committee on Religious Liberty, told EWTN News Nightly June 26.

"The Church and its religious organizations serve millions of people with love and attention," the archbishop said, adding that "it would be a shame to see that jeopardized. It would be a shame to see free exercise swallowed up in this decision."

In a 5-4 decision on Friday, the Supreme Court ruled on Obergefell v. Hodges, deciding that states must grant marriage licenses to same-sex couples, and recognize same-sex marriages conducted in other states.

The ruling was granted under the Fourteenth Amendment, which protects the rights of all citizens to "life, liberty, or property" under due process, and guarantees them equal protection of the laws in the states.

In this case, the Court ruled that the state laws defining marriage as between one man and one woman deprived same-sex couples of their right to legally marry.

The ruling overturned a November decision by the U.S. Sixth Circuit Court of Appeals that upheld traditional marriage laws in Michigan, Ohio, Kentucky, and Tennessee. Same-sex marriage is now legal in all fifty states. States must also recognize one another's marriage licenses regardless of the partners' sexes.

Military chaplains will be protected by the First Amendment, Archbishop Timothy Broglio of the Archdiocese for the Military Services told CNA.

"In general, chaplains enjoy the First Amendment rights that all of us enjoy. And so they are forbidden to do anything that their endorser - or in this case, for Catholic priests, that would be me - forbids them to do, and they must the ability to do the things that the endorser requires of them. So at least on the legal level, they are protected."

What is less clear is the other consequences the decision brings upon the military archdiocese, Archbishop Broglio said, conceding that problems previously unseen will now manifest themselves.

Though it is also unclear how the ruling will specifically affect Catholic individuals, families, businesses, and ministries, it is clearly far-reaching, Archbishop Lori said. It will affect a myriad of marriage laws and regulations at the state and local levels.

"Today's ruling does not just affect one law, but in fact hundreds if not thousands of federal, state, and local laws and regulations that implicate marriage, spouses, and so forth," he said. People of faith who believe in the traditional understanding of marriage " may very well see a difficult road ahead."

Anthony Picarello, general counsel for the U.S. bishops conference, addressed some specific areas where controversies might arise, such as tax exemptions, employee benefits, employment, and school accreditation.

"We've seen already many of these disputes emerge in states that have already recognized same-sex marriage. We've seen them in states that have aggressive sexual orientation, gender identity, and anti-discrimination laws," he commented.

There will likely be social consequences for supporters of the traditional understanding of marriage, Picarello added.

The Supreme Court's decision "makes a nod in the direction of religious liberty but not enough of one," Archbishop Lori said.

While it grants the right of religions to teach and advocate about marriage, the majority opinion says nothing of the free exercise of religion that is central to the First Amendment - and this is extremely problematic, the archbishop explained.

The free exercise of religion means the ability for people to live their religious beliefs while "interacting with the broader society," Archbishop Lori continued. For the majority of the court to omit this in its discussion of religious freedom could "give rise to a lot of legal controversies," he warned.

Catholics must vigorously defend this right of free exercise, while respecting the beliefs of opponents, he added.

"To put a label on people as a way of closing off the debate, or as a way of vilifying those who disagree, really runs counter to what the First Amendment intends," Archbishop Lori said.

"As believers, we should be prepared, whatever the cost is, to bear witness to our faith. To do it lovingly, but also to do it truthfully and to do it persistently."

Catholics should take heart that this is not the first time they have faced the prospect of persecution in the U.S., Archbishop Broglio added.

"This wouldn't be the first time that we've experienced ostracism for our beliefs. All you have to do is go back to the 19th century with the Know Nothings and the reactions there," he said.

"So we survived that. We'll survive this."