When the Boy Scouts of America announced Monday that transgender boys would be welcome to camp, hike and earn merit badges alongside their peers, the move brought praise from critics of the organization who for years have called for more inclusive membership rules.

But the decision, which came with little warning and reversed a more than century-old stance of determining gender based on birth certificates, further alienated many religious conservatives who were longtime advocates of the program.

“Now we see once again that the Boy Scouts really is committed to a gender-theory culture war that evangelical Christians and many other Americans just can’t accept,” said Russell Moore, the president of the Ethics & Religious Liberty Commission, the public policy arm of the Southern Baptist Convention.

Mr. Moore, a former scout, said Southern Baptist churches and others had been dismayed by Boy Scout policies for several years, as the Scouts moved first to allow openly gay youth members, and then openly gay adult leaders. Though several Southern Baptist congregations have stopped sponsoring Scout troops, Mr. Moore said others had held out hope that the organization would return to a more conservative worldview.