One afternoon during the first week of classes this week at Xavier High School in Manhattan, as the various student clubs reconvened, Joseph Papeo walked into Alexander Lavy’s physics classroom. On the walls hung a crucifix and posters of Einstein and Homer Simpson. Two flags flanked the door. One was the American standard, while the other was the rainbow banner of gay pride.Mr. Papeo, 17, was in the classroom for a meeting of Xavier’s Gay-Straight Alliance. A senior and the club’s co-president, Mr. Papeo positioned himself at a dry-erase board, preparing to write a list of the recent milestones for gay rights at Xavier and in the rest of the world.