Four months ago, in a decision allowing a former minister's employment discrimination lawsuit against Gannon University to proceed, a three judge panel of the U.S. Court of Appeals broke with a legal precedent widely embraced by other federal courts that generally shielded religious organizations from employment claims brought by clergy. The court's decision was applauded by some advocates for women's rights but strongly challenged by legal experts, who said its ruling against the Roman Catholic college in Pennsylvania would never hold up.

They were right. Wednesday, a different three judge panel of the Third Circuit -- convened after one of the original judges died, another recused himself, and the first decision was vacated by the full appeals court -- issued an opinion in which it thoroughly endorsed the "ministerial exception" and sided in almost every way with Gannon and against Lynette M. Petruska, the former chaplain who had sued Gannon in 2004 for alleged sex discrimination, retaliation, and breach of contract, among other things when it essentially reorganized her out of a job in 2000.

Evan C. Rudert, a lawyer representing Gannon, described as "highly extraordinary" the Third Circuit's decision to more or less junk the original decision and allow a new three judge panel -- led by the one judge who dissented from the original panel's ruling -- to consider the case anew. Other legal experts echoed that conclusion.

"Of course we believe it is the right decision, which is the reason why when the first decision came down, we petitioned for rehearing," Rudert said. "This decision is consistent with the law of every other circuit that's ruled on the issue, and it protects religious institutions' right to choose who performs spiritual functions."

That's not how the Third Circuit saw it the first time around, in its ruling in May. In a 2 to 1 ruling, the original three judge panel concluded that Petruska had a right under Title VII of the Civil Rights Act to pursue her claims that Gannon had decided to restructure its administrative ranks to make Petruska report to a male administrator because she had pushed for an aggressive review of the university’s sexual harassment policies and helped bring to light alleged misbehavior by senior officials at the institution.

The court acknowledged that the so-called ministerial exception permitted religious institutions to engage in otherwise illegal discrimination when it made decisions based on “religious belief, religious doctrine, or the internal regulations of a church,” but said that "where a church discriminates for reasons unrelated to religion, we hold that the Constitution does not foreclose Title VII suits.” Employment discrimination by a religious institution that is not based on religious belief or doctrine is “simply the exercise of intolerance, not the free exercise of religion that the Constitution protects,” the majority ruled.

Gannon asked the Third Circuit to reconsider the original ruling, and in June, the court made the extremely rare decision to let another three judge panel rehear the case. (More common, though still rare, is for an entire circuit court to rehear a case.) The case was reargued in August, in a "significantly different climate," Rudert said.

Wednesday's opinion, which was written by Judge D. Brooks Smith, the dissenting judge in the first decision, said that the "ministerial exception, as we conceive of it, operates to bar any claim, the resolution of which would limit a religious institution's right to select who will perform particular spiritual functions." The protection ensured by the Constitution's Free Exercise Clause applies not just to a religious college's or other institution's selection of its clergy -- "who will carry its spiritual message necessarily infringes upon its free exercise right to profess its beliefs" -- but also to "the church’s right to decide matters of governance and internal organization," the Third Circuit said.

So Gannon's decision to restructure in such a way that Petruska felt undermined her position as university chaplain, the court said, was covered: "The Vice President for Mission and Ministry and the University Chaplain at Gannon both serve spiritual functions -- in other words, the primary duties of those employees include “teaching, spreading the faith, church governance, supervision of a religious order, or supervision of participation in religious ritual or worship. Accordingly, Gannon’s decisions regarding who to install in those positions and the manner in which their duties would be divided were decisions about who would perform those constitutionally protected spiritual functions. Those choices are protected from governmental interference by the Free Exercise Clause."

Although the Third Circuit panel barred Petruska from suing Gannon on five of her six claims, it did clear the way for her to pursue her claim that the university violated state contract law by changing her job responsibilities. "On its face," the court ruled, "application of state contract law does not involve government-imposed limits on Gannon's right to select her ministers: Unlike the duties under Title VII and state tort law, contractual obligations are entirely voluntary.... Enforcement of a promise, willingly made and supported by consideration, in no way constitutes a state-imposed limit upon a church's free exercise rights."

Neither Petruska nor her lawyer could be reached for comment for this article.