Back in the 1830s Andrew Jackson said: John Marshall has made his decision; now let him enforce it! Laws can be written, but what's the enforcement mechanism? Who is going to be out seeing the laws are followed to the letter? How hard is it to give another reason - not qualified enough, overqualified, too mellow, too stressed out. Proving something in court is not always open and shut. Granted there was the McDonalds that made that stupid phone call to the trans applicant - but that was one story, I don't see them every day as people who get paid to do HR are pretty tuned into what they can and can not say.
And there is a religious exemption (of course), a huge one.
The Employment Non-Discrimination Act (ENDA) includes a broad exemption for religious organizations. ENDA's religious exemption recognizes that the U.S. Constitution protects certain employment decisions of religious organizations and that some religious organizations may have a specific and significant religious reason to make employment decisions, even those that take an individual's sexual orientation or gender identity into account. It also acknowledges that gay, lesbian, bisexual and transgender (LGBT) employees of religious organizations should be aware that they could lose their jobs, even jobs that do not serve a clearly religious function, because of sexual orientation or gender identity.
The exemption consists of three parts:
A complete exemption for houses of worship, parochial and similar religious schools, and missions
A codification of the so-called "ministerial exemption" recognized by many federal courts, exempting positions at religious organizations that involve the teaching or spreading religion, religious governance, or the supervision of individuals engaged in these activities
A provision allowing religious organizations, for classes of jobs, to require employees and applicants to conform to a declared set of significant religious tenets, including ones which would bar LGBT people from holding the position
In the third section of the exemption, the declaration of an employer's significant tenets is not subject to judicial review and is only applicable in proceedings under ENDA.
In practice, this language continues to exempt many jobs with religious organizations. Under the first section of the exemption, for example, a priest or minister is clearly exempt, as well as the church secretary and the administrator of Sunday School programs. Under the second paragraph, the chaplain at a religiously-affiliated hospital and the teacher of canon law at a religious university are also exempt.
Under the third part of the exemption, a religious corporation, association, educational institution, or society may decide to apply its religious tenets to classes of employees. Although this provision gives, as most courts would give, deference to religious organizations in declaring significant religious tenets, it means that ENDA will apply to some positions but not others at these employers. For example, a religiously-affiliated hospital could choose to require all nurses to follow a declared set of significant religious tenets, including avoiding same-sex sexual activity, and be able to terminate a male nurse who they subsequently learn is in a relationship with another man. Similarly, a social services agency run by a religious sect could require its executive director to subscribe to a set of tenets that it declares significant, including one that bars LGBT people from holding the job, but choose not impose the same requirement on its social workers or other classes of employees
So no one is going to be forcing churches to hire anyone.