IANAL, but if I had to guess...
Diskeeper is probably arguing from Corporation of Presiding Bishop v. Amos. A gym open to the public but affiliated with the Church of Latter Day Saints fired a janitor who wasn't a Mormon. The janitor sued, arguing the exemption for religious organizations from Title VII of the Civil Rights Act (prohibiting religious discrimination in employment) violated the establishment clause of the 1st amendment. IIRC, the Church argued that this exemption was a permissible accommodation of the Church's free exercise rights under the 1st amendment. The Supreme Court agreed with the Church.
The problem is, Diskeeper isn't a religious organization, so they don't qualify for the statutory exemption in Title VII. While religious instruction in the workplace may or may not be lawful, making continued employment dependent on religious instruction in a particular faith almost certainly is unlawful.
Hopefully Diskeeper goes down at the summary judgment stage, if not on a motion to dismiss.