NEW YORK — Conservative faith leaders have made religious liberty a rallying cry as gay marriage has spread throughout the states. And though stunned by Indiana’s retreat from a religious freedom law after an uproar over same-sex marriage, they vow not to give up.

Evangelical and Roman Catholic leaders say they will continue their push for conscience protections from laws they consider immoral — a drive that gained momentum several years ago when they saw their beliefs on marriage, abortion and other issues increasingly in the minority.

Archbishop William Lori of Baltimore, who leads the religious liberty committee of the U.S. Conference of Catholic Bishops, said the bishops’ goals have not changed following the uproar this week in Indiana and to a lesser degree Arkansas.

“Individual or family-owned businesses as well as religious institutions should have the freedom to serve others consistent with their faith,” Lori said in a statement.

Similarly, the Rev. Russell Moore, who leads the public policy arm of the Southern Baptist Convention, said, “We have to continue to press for religious liberty for everybody regardless of how unpopular that concept might be.”

Still, Tim Schultz, president of the 1st Amendment Partnership, which works with religious groups and state lawmakers on religious liberty, said after this week’s controversy over religious freedom, “the brand has definitely been tarnished.”

The governors of Indiana and Arkansas signed bills Thursday hoping to quiet the national outcry over whether the laws offered a legal defense for discrimination against gays. In Arkansas, the changes more closely aligned the bill with the 1993 federal Religious Freedom Restoration Act. The Indiana law was amended to bar a religious liberty defense by for-profit businesses accused of discrimination for refusing to serve someone based on sexual orientation, but left in place protections for faith-based nonprofits.

Religious liberty was once an issue that consistently united groups across the political and theological spectrum. But religious conservatives came to adopt religious freedom as a call to arms, as they found themselves more and more on the losing side of the culture wars.

A decade ago, the Becket Fund for Religious Liberty, a public interest law firm in Washington, convened legal scholars from across the ideological divide on gay marriage to examine potential areas where religious freedom and gay rights might clash.

First Amendment protections for worship are secure. But complications arise when faith-affiliated organizations, such as charities, hospitals and schools, try to maintain their religious identity even as large employers of people from all faiths and providers of services to the public.

The 2005 Becket meeting generated a book, “Same-Sex Marriage and Religious Liberty: Emerging Conflicts,” and a subsequent policy paper that became influential among church-state experts and religious leaders closely watching the issue.

By 2011, the Catholic bishops’ conference had formed its own religious liberty committee and started organizing rallies and prayer services around the issue.