If legal action is taken, this one could well go to the Supreme Court:
Mom-to-be claims she was fired from Baptist church for not scheduling wedding date | Fox News
Earlier, SCOTUS rebuked Obama's attempts to have these terminations automatically reviewable by the government 9-0 (Tabor Lutheran vs EEOC). But, some justices also said the ministerial exemption, though broad, is not all encompassing. They then welcomed further cases.
In this case, the woman is a day care worker, a position that may, or may not be considered "ministerial". In my opinion, if one accepts employment of any kind at a non profit (church, mosque, temple, PETA, etc), you play by their rules, or you dont play there.
As a side note, there was a similar one with a Catholic dioceses, but the diocese offered a modest settlement (and in doing so placed their First Amendment rights in danger), and the case was dropped.