The Arizona governor’s decision Wednesday to veto a bill widely seen as pitting religious protections against gay rights puts an end to two controversial amendments proposed by lawmakers.

But it leaves standing the state’s Religious Freedom Restoration Act, which continues to empower individuals to sue when they believe state or local laws – including antidiscrimination laws – are violating their religious rights.

In announcing her decision to veto the amendments, known as SB 1062, Gov. Jan Brewer (R) said that religious liberty is valued in Arizona. She added that the state also values the principle of nondiscrimination.

How those two goals coexist in Arizona in the future remains unclear. But it is clear from the governor’s veto that the potential downside of following through with the amendments outweighed the advantages.

“I sincerely believe that SB 1062 has the potential to create more problems than it purports to solve,” she said in a brief statement.

While the Brewer veto ends the current dispute in a way that appears to deliver a clear victory to gay rights advocates and their supporters, the underlying causes of the conflict remain unresolved.

On one side are Arizona residents seeking to live their lives in accord with traditional moral positions embraced in the Bible’s Old Testament – positions that condemn homosexuality. On the other side are gay men, lesbians, bisexual, and transsexual individuals fighting for equal rights and equal dignity in communities they also call home.

The Arizona Religious Freedom Restoration Act (RFRA) seeks to protect religious faith from coercive laws. That protection continues to exist throughout Arizona.

What is changing is a growing recognition of civil rights for gay Americans that is clashing with traditional religious teachings. For example, Arizona law offers no protection against discrimination based on sexual orientation, but three Arizona cities – Phoenix, Tucson, and Flagstaff – have passed ordinances banning sexual orientation discrimination in their jurisdictions.

The two proposed amendments to the Arizona RFRA were an attempt to address the issue in a way that favored religious adherents. Brewer’s veto eliminates the attempt, but it does nothing to address the underlying clash.

The veto was issued amid a growing controversy in Arizona over what had been a little-noticed state law patterned on a 21-year-old federal statute designed to shield religious adherents from government measures that violate their beliefs.

The original Religious Freedom Restoration Act, far from a hate-inspired antigay measure, sailed through the US House of Representatives on a voice vote and passed the US Senate 97 to 3 before being signed into law by then-President Bill Clinton in 1993.

The law was written to fill a vacuum left after the US Supreme Court embraced a significantly narrower reading of the protections of religious liberty under the First Amendment’s free exercise of religion clause. Congress responded with RFRA.

Arizona passed its own version of RFRA 15 years ago, and has apparently avoided any outcry over its provisions until last week, when lawmakers approved two amendments to the state RFRA statute.

Critics said the SB 1062 amendments would grant religious individuals a right to discriminate against gay men and lesbians. They threatened boycotts and other public-relations retaliation against Arizona unless Brewer vetoed the bill.

“Arizona’s legislature has reached a new low by awarding special legal protection to businesses and individuals that discriminate against LGBT people,” Graeme Reid, LGBT rights director of Human Rights Watch, said in a statement issued before the Wednesday veto.

“Governor Jan Brewer’s failure to veto this bill would not only be disastrous for Arizona, but would be likely to spur such odious legislation in other US states,” he said.

Amid the accelerating outcry, supporters of the measure had been few and far between, often trying to dodge the media rather than defend the bill.

Among the few standing up for the proposed law were a group of 11 constitutional scholars.

In a four-page letter sent this week to Brewer, the scholars said the Arizona law had been “egregiously misrepresented by many of its critics.”

“Some of us are Republicans; some of us are Democrats. Some of us are religious; some of us are not. Some of us oppose same-sex marriage; some of us support it,” the letter said.

Nine of the signers of the letter said they supported the legislation; two were not sure. “But all of us believe that many criticisms of the Arizona law are deeply misleading,” the letter said.

The federal government and 18 states have Religious Freedom Restoration Acts on their books. More than 12 other states have interpreted their state constitutions to provide similar protections to religious individuals.

Under the Religious Freedom Restoration Act, the government is barred from imposing a substantial burden on a person’s exercise of religion unless the government can offer a compelling justification for the burden and then minimize the burden as much as possible.

The law empowers individuals to challenge government laws that infringe upon the exercise of their religious beliefs. It also provides a defense for someone who claims that a neutral, generally applicable law is forcing them to choose between fidelity to the law or fidelity to their religious beliefs.

It is that dilemma that forms the basis of two cases set for argument next month at the US Supreme Court. Both cases test the power of the federal government to force business owners to provide their employees with contraceptives that the owners say violate their religious faith.

The owners are suing the federal government under the federal RFRA, arguing that the government burden on their religious beliefs violates RFRA and their right to freely exercise their religion without government interference.

The Arizona statute sought to provide the same protections at the state and local level. But the lawmakers wanted to clear up two potential ambiguities. The first amendment was designed to make clear that Arizona’s RFRA would cover instances when a state or local government measure requires a person to violate their religious beliefs while conducting their business.

The second amendment sought to make clear that RFRA protects individuals who are sued by a private citizen seeking to enforce a state or local measure that would force them to violate their religious faith.

“To be clear: SB 1062 does not say that businesses can discriminate for religious reasons,” the scholars said in their letter.

The proposed amendments provided a defense for a business owner or allowed a business owner to file a lawsuit to enforce RFRA protection. But it is ultimately up to the Arizona courts to decide if such protection is warranted or not, they said.

The scholars said the Arizona statute was substantially different than a measure under consideration in Kansas that has also sparked protests and significant media attention. Rather than a broadly applicable standard, the Kansas bill requires that in any confrontation between gay rights and religious objections, the religious objector would always win.

“The real problem with the Kansas bill is not that it proposes a specific rule, but that it proposes a very one-sided and unfair rule,” the scholars said.

“We agree with Congress and a clear majority of states that government should not burden a person’s religious practice without a compelling interest,” they said in the letter. “But sometimes government does have compelling interests, and then religious practices must be burdened. The Arizona bill recognizes that; the Kansas bill does not.”

The scholars added: “People claiming that the two bills are similar are simply smearing the Arizona bill, disregarding the long and successful history of state and federal RFRAs.”

Among the 11 signers of the letter are Stanford law professor and former appeals court Judge Michael McConnell, Virginia law school professor Douglas Laycock, Harvard law professor Mary Ann Glendon, and Notre Dame law professor Richard Garnett.