In Alabama, Mr. Trump worked both sides, backing the establishment’s candidate, Senator Luther Strange, in the Republican primary, then disregarding his political advisers and campaigning for Mr. Moore, even after allegations surfaced that he had sexually assaulted or molested girls as young as 14.

The tableau of Mr. Trump working at cross purposes with his populist allies was awkward. Before Mr. Trump endorsed Mr. Moore, White House aides pressured Sarah Palin, the party’s 2008 vice-presidential nominee and a friend of both Mr. Bannon and Mr. Trump, not to campaign for the former judge. As Ms. Palin rode in the back of a car to a Moore rally in Montgomery on Sept. 21, her cellphone rang. Seeing the Washington area code 202 flash on her caller ID she groused, “It must be the White House.” She ignored the call, said one person who had spoken with Ms. Palin.

Mr. Trump’s dilemma has also become an identity crisis for many in the conservative movement. Groups across the right, many of which have been intensely antagonistic toward party leadership, find themselves in a position to work on legislation that can actually pass in a Washington under total Republican control. For that, they need relationships with the leaders in the party that Mr. Bannon and other conservatives want to supplant.

In Alabama, most of the groups in the conservative coalition that usually defend Republican Senate candidates were conspicuously absent even before assault allegations surfaced. Anti-abortion groups, evangelical Christian organizations and even the National Rifle Association, which spent just $55,000 opposing Mr. Moore’s opponent, Doug Jones, were largely quiet.

The same pressure to cooperate with the establishment will complicate the runs of Bannon-backed Senate candidates like Chris McDaniel in Mississippi and Kelli Ward in Arizona, whom Republicans are already criticizing as unfit for office, especially if they become the party’s nominees.

Conservative leaders who have been allies of Mr. Bannon’s said they worry that disputes over candidates will only weaken Republicans in an environment of Democratic enthusiasm that is already putting the party at a disadvantage.

The Democrats “are coming,” said Ralph Reed, founder of the Faith and Freedom Coalition. “They are coming in big, big numbers. And they are coming with an intensity that is roughly where we were in ’94 and 2010.”