Michael Dwyer, Associated Press

With a recent executive order, President Obama prohibited discrimination based on sexual orientation in the hiring of those working under federal contract without clearly including protections for the free exercise of religion.

The order amends a 1965 order by President Lyndon Johnson prohibiting some forms of discrimination by federal contractors. With Obama’s addition in italics, the amended order now prohibits contractors from discrimination “against any employee or applicant for employment because of race, color, religion, sex, sexual orientation, gender identity or national origin.”

Those who had sought faith-based protections make several points. First, in 2002, President George W. Bush made clear, in Executive Order 13,279, that faith-based contractors may restrict hiring to members of their own faith.

Second, in 2007, a memorandum by the Office of Legal Counsel of the Attorney General said that the Religious Freedom Restoration Act “is reasonably construed” to protect religious organization that administer federal funds through social service programs from religious nondiscrimination requirements imposed on other federal grantees.

Third, it’s important to note that there are considerable differences between federal contracts and federal grants. Many religious organizations – such as Catholic Charities, World Vision and World Relief – partner with the federal government, but usually through federal grants, which are not affected by the executive order.

Religious organizations comprise a miniscule part of the federal contract program, used for goods and services in the military, security, transportation and the like.

Douglas Laycock, professor of law and religious studies at the University of Virginia, said that past orders sustain a patchwork of protections for religious organizations. “And very important, the executive order creates no right for anyone to sue anyone else,” he told Christianity Today. “So gay rights groups cannot organize litigation against religious contractors. Only the contracting agencies can enforce this order, and they may quietly enforce it with attention to religious liberty – which is what this administration has mostly done so far.”

Still, there will be questions in the application and interpretation of the order, as reported in the Deseret News’ National edition.

Meanwhile, Michael Wear — Obama’s own 2012 campaign faith advisor — said “we risk opening up the doors for litigation that leaves both LGBT Americans and religious organizations uncertain and unprotected.”

Pastor Robert Jeffress of Dallas’ First Baptist Church told Fox News his fears of where lies the next battlefield: “The problem with their executive order is that it paves the way for the next one, which could withhold the tax-exempt status or broadcast status or broadcast licenses for the religious organizations holding biblical believes with which the administration disagrees.”

Wear helped draft one of two major letters from faith-based leaders earlier this summer, seeking the continuation of protections for religious freedom. Together with Dr. Rick Warren of Saddleback Church, the CEO of Catholic Charities USA and others, Wear framed the question this way: “While the nation has undergone incredible social and legal change of the last decade, we still live in a nation with different beliefs about sexuality. We must find a way to respect diversity of opinion …. When the capacity of religious organizations is limited, the common good suffers.”

The other major group of religious freedom advocates, including professor Laycock and Michael McConnell, director of the Constitutional Law Center at Stanford University and former 10th U.S. Circuit Court of Appeals judge, made specific reference to the strong religious freedom protections included in the Employment Non-Discrimination Act passed by the Senate in November 2013.

ENDA, which has not passed the House, was propelled forward by this declaration: “This Act shall not apply to a corporation, association, educational institution or institution of learning, or society that is exempt from the religious discrimination provisions of title VII of the Civil Rights Act of 1964.”

These same provisions should be included in the Obama administration’s executive order on federal contracting.