This month, the Boy Scouts ordered the dismissal of Mr. McGrath, a software engineer who is married to his longtime partner, after he spoke about his sexual orientation in a news article profiling the troop, which was formed last year in a south Seattle neighborhood heavily populated by immigrants and lower-income families. The decision to disenfranchise the organization, sent in a letter on Friday, came after church officials said they would continue to support Mr. McGrath and had no intention of following the order.

“Because the church no longer agrees to the terms of the B.S.A.-chartered organization agreement, which includes following B.S.A. policies, it is no longer authorized to offer the scouting program,” a spokesman for the Boy Scouts, Deron Smith, said in an emailed statement on Monday. “We are saddened by this development.”

The debate over whether to allow gays in scouting has been a grim one for the Boy Scouts, which has prided itself for generations on its assertions that scouting builds character and integrity, even as revelations in recent years about sexual predators in the ranks have exploded in court cases and news coverage. The scandals have made the organization sensitive about choosing leaders, many people involved in scouting said, especially as scout numbers have declined. Last year’s policy shift, to allow gay youths, sharply divided the religious community in particular.

Mr. McGrath, who is on vacation in Italy, said in a telephone interview that discussions were already beginning about what might come next for the youth organization at Rainier Beach. However, Mr. Smith, the Boy Scouts spokesman, said in his statement, “We have already identified a new chartered organization to sponsor the units and are contacting the parents and leaders of the units to inform them of the change.”

Mr. McGrath described his church’s youth group as diverse. He said there were boys from immigrant families, including from Asia and Africa, as well as two boys with gay fathers.