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"The three-judge panel didn't rule on the merits of the case; it only refused to allow the university to opt out of the provision as its lawsuit makes its way through the courts."

I'm confused - what other courts are involved? Why would the appeals court make a ruling if the case hadn't worked its way to the appeals court?

It means Notre Dame will appeal the the Supreme Court.

Presumably, Notre Shame sought a preliminary injunction against enforcement of the contraceptives mandate pending determination of the case on the merits. That request was denied by the federal district court judge and Notre Shame appealed to the 7th Circuit Court of Appeals which denied the appeal (such appeals as to injunctions are verrrry seldom granted). Notre Shame appealed to SCOTUS which did not rule on the injunction itself but sent the matter back to the 7th Circuit for another determination. The 7th Circuit remained adamant and left the status quo of no injunction which superficially seems to resist SCOTUS which had already decided in Hobby Lobby's case that even nominally secular corporations owned by believing Christians cannot be compelled to abide by the contraceptives mandate of Obozo"care."

Leaving aside the question of whether any actual Catholic would regard Notre Shame as Catholic, and, despite Judge Posner's outstanding reputation as a conservative jurist of libertarian sensibilities, it seems likely that SCOTUS will, under some rubric, grant some relief. The classic tests are likelihood of prevailing on the merits (Hobby Lobby makes this very likely and was decided apparently after the district court refused the injunction) and secondly weighing the "equities": i.e. would granting the injunction harm the government more than denying it would hurt the university.

A request for a preliminary injunction is a request for extraordinary remedy, typically to freeze the status quo pending resolution at the trial level of the case in chief on the merits. Given the glacial pace at which most federal cases proceed, great harm could be sustained by Notre Shame during the pretrial years. The government can probably live with an adverse result more easily.

Caveat: the ABC news report is sketchy and I have not read the actual decisions and dissents.