Christian colleges and universities also have to consider Title IX of the Higher Education Amendments of 1972: "No person in the United States shall, on the basis of sex, be excluded from participation in, be denied the benefits of, or be subjected to discrimination under any education program or activity receiving Federal financial assistance."

It’s a short hop from defining “sex” to include orientation and gender identity for Title VII purposes to finding the same in the case of Title IX. A school in violation of Title IX could lose its tax-exempt status and substantial government funding.

"The fear is so large in many institutions because 40 or 50 or maybe even 60 percent of their budgets are really coming from the federal government," says Dale Kemp, the chief financial officer at Wheaton College in Illinois and the speaker at the CCCU session. "To think they could survive without that [funding] would be catastrophic."

Just ask Bob Jones University about the costs of crossing the feds. BJU lost its tax-exempt status due to its ban on interracial relationships in a Supreme Court ruling that resulted in BJU paying $1 million in back taxes.

None other than Justice Samuel Alito has drawn a parallel to the current clash.

In April 2015, during a Supreme Court argument over the constitutional rights of LGBT individuals, Justice Samuel Alito noted that Bob Jones University in South Carolina had lost its tax-exempt status because of its prohibition on interracial dating and marriage. "Would the same apply to a university or a college if it opposed same-sex marriage?" Alito asked then-U.S. Solicitor General Donald Verrilli Jr. "It's certainly going to be an issue," Verrilli answered. "I don't deny that."

Christian schools noted the possibility that their anti-LGBTQ policies could land them in trouble with the federal government. More than that, they registered the likelihood that LGBTQ rights would continue to expand, creating additional implicit duties and prohibitions, rather than shrink.

The exchange alarmed officials at conservative religious schools, for which the loss of tax-exempt status or federal funding would be devastating. Their anxiety deepened a year later, when the Obama administration notified colleges and universities that it interpreted Title IX as prohibiting discrimination "based on a student's gender identity, including discrimination based on a student's transgender status." Christian schools saw that letter as threatening a loss of federal funding if they refused to accommodate students who identify as transgender and want to be housed with other students who share their gender identity. Upon taking office, the Trump administration rescinded the Obama directive, but some leaders at Christian schools still fear the cultural and legal trends are in favor of expanded LGBT rights on their campuses, which could mean their policies on sexual behavior could face serious challenges.

There are schisms within the schools, between students and faculty, for example, but also among the schools, with some readier than others to adapt more progressive policies.

It’d be a heavy lift to replace 40-50 percent of 130-plus institutions’ funding. The question is, which schools will fall in line with federal rulings, which will struggle, and which will fold?