Even if the day care is in the church, some justices could well rule her way. In Tabor Lutheran vs EEOC, the more liberal justices said the ministerial exemption" that churches enjoy should only apply to employees with clear religous or at least quasi religous roles. Conservative justices implied the exemption was for any employee.
That being said, my guess is that she will lose at SCOTUS. The conservative justices think any employee should be covered. Even some of the liberal ones will either want to err on the side of the first amendment, or wont want to get bogged down in debates if a day care worker is, or is not a religous role. For example, what if whe reads childrens' bible books as part of her duties, would that make her a "minsiter" etc etc.