(a) Nondiscrimination is preserved (No one possesses a "get out of jail free" card as Mike suggests)
(b) Some reasonable form of self recusal is possible (No one possesses a "put someone in jail free" card)
Similar standards are applied in professional codes of ethics all the time.
Certainly there are historical examples where religious freedom has been appealed to inappropriately. But it does not necessarily follow that any appeal to religious freedom today is therefore without merit. That line of thinking leads to a place where religion or moral conviction is completely dismissed as a valid basis for taking a position. That is a dangerous place for everyone.