Regulators, courts, and the public are rapidly losing their understanding of and respect for some of the core countercultural practices of religious organizations, some of the distinctive ways they operate internally and some of the distinctive ways they serve the public. Governments at all levels are enacting more and more nondiscrimination requirements that conflict with these key countercultural practices while also becoming more reluctant to provide exemptions to the requirements.

One sign of this trend: When the Employment Nondiscrimination Act, designed to stop job discrimination on the bases of sexual orientation and gender identity, was adopted by the Senate a year ago (and then stalled in the House), it entirely exempted religious organizations from its new rules and prohibited governments from excluding those religious organizations from federal funding programs because of their exemption. In sharp contrast, when President Obama issued his Executive Order in July to forbid the same kinds of job discrimination by federal contractors, he pointedly did not exempt religious organizations from the new prohibitions, making it unclear whether such organizations will be excluded from this type of federal funding if they hold their employees to a conservative sexual conduct standard.

And that refusal to fully respect the distinctive, faith-shaped, employment practices of many religious organizations is President Obama’s stance even though he has maintained the main principles of the faith-based initiative, an initiative designed to ensure that faith-based providers are not excluded from partnerships with the federal government.

The Obama administration straddles two trends, two commitments: on the one hand, a deep and growing commitment to advancing LGBT rights whenever and wherever possible; on the other hand, an understanding of the important role played in civil society by faith-based organizations, coupled with a desire not to harm the ability of these organizations to play that role. But the latter commitment is no proof against the former, witness not only the President’s LGBT Executive Order without a religious organization exemption but also his administration’s fierce and even dysfunctional clinging to its three-category treatment of religious organizations in the case of the contraceptives mandate (roughly: churches are exempt, religious nonprofits get attenuated respect for their convictions, and companies of religious conviction will get only minimal religious freedom protections, and that only because of the US Supreme Court’s insistence).

The United States has entered a time of sorting. Which faith-based organizations will prove to be so committed to their religious principles and countercultural practices that they will advocate for the freedom they themselves and all such organizations need? And which faith-based organizations, while preferring to stick with their historic religious character, will prove to be unwilling or unable to withstand the public opprobrium of being clearly religious and different, won’t adopt the internal overt religious practices needed to claim religious freedom protections, and will then gradually succumb to secularizing public pressures and government rules?

This is the time for faith-based organizations to lift up the faith flag: to make sure that their internal policies are transparently based on religious convictions and that their practices are consistent with the stated convictions; to make it clear to the public — winsomely– that the organization is faith-based, faith-shaped. The point is not to retreat to a religious ghetto but rather to continue to serve the public in a faith-shaped way.

Now is the time to lift up the faith flag: to speak up, to rally around organizations that are being pilloried, for organizations to bolster their faith identity. When many wave the faith flag, it will be clear to the public and to public officials that what is at stake in the battle for institutional religious freedom is a large swathe of our civil society, a large proportion of the organizations that foster the common good.

How our society will balance out nondiscrimination requirements with religious freedom is not yet obvious: we are in the middle of a huge wrestling match. If religious organizations let LGBT and secular extremists occupy the public discussions and public policymaking, then they shouldn’t be surprised if even more of the public comes to agree that faith-based organizations are marginal institutions seeking to do what is plainly wrong. There must be faith voices in the conversation!