Chief Justice Roberts was the initial one to raise the issue of the Church and the Priesthood. Breyer was just chiming in after the fact.
I can't see this Court daring to wade into the morass of determining qualifications for membership or leadership of religious organizations. I'm cautiously hopeful that the Court will kick the Obama administration square in the forehead with at least a 7-2 vote--maybe even 8-1 (Sotomayor is so stupid and arrogant, I can't accurately predict what that idiot might do).