The following weeks played out like a Hollywood script: two suspects turned state’s witnesses, and one of them escaped and was on the loose for almost three days before being caught. Ultimately, on July 8, only the 23-year-old gunman was indicted on two counts of first-degree murder and 10 counts of attempted murder, “motivated by feelings of revenge and anger” and “hostility toward the victim’s sexual orientation,” according to the indictment.

“The news was confusing, is still confusing” Ms. Nir said.

Mr. Uchovsky said, “It’s very embarrassing.”

Since the shooting, much of the country seemed to be sharing in the gay community’s blossoming pride. But now many gay men and lesbians are on the defensive, struggling to address the sordid allegations, while some right-wing politicians accuse the community of crying wolf. Most gay men and lesbians, speaking in the news media or on social networks, are still adamant that the crime was driven by deep homophobia and deserves the distinction of a hate crime, an argument the indictment appears to accept.

But not everyone agrees.

“People don’t question whether it was a hate crime,” said Alon Shani, a reporter for Israeli television who covered the case when it occurred and who also identifies with the L.G.B.T. community. He thinks gay leaders have clung to the narrative of a hate crime for so long that they don’t dare let go. But with hate crimes, he points out, motives matter. And until the case is argued in court and a verdict is handed down, there’s simply no way to know for sure.

As uncomfortable as it is to say, there is a certain “loss in terms of P.R. value” when what seemed like a clear-cut hate crime narrative turns out to be marred, said Shuki Cohen, an assistant professor of psychology at John Jay College of Criminal Justice in New York. Dr. Cohen, born in Israel, counts himself as a member of the L.G.B.T. community as well. For many minorities, he said, “our suffering is our identity card.”

Mr. Uchovsky admits: “It’s not so good when you have to hang onto a massacre. Same way I don’t think we have to cling to the Holocaust to explain why Israel should exist.”