The protest against comments by Lt. Gen. William Boykin, a senior Pentagon official, could have calmed by now had Secretary Donald Rumsfeld not waffled on the inappropriateness – in fact, the harmfulness – of the remarks. It was not until President Bush made a clear statement that turning the war against terrorism into a religious war was unacceptable that the defense secretary somewhat clarified himself. But by then the issue had grown beyond a single poorly made statement into a pattern of comments that incite U.S. opponents to act against this nation.

As a factual matter, it has been only an extremist minority of Muslims that has tried to hijack one of the world’s great religions to organize a jihad or holy war against the United States. To accept the conflict in those terms is to play right into the hands of Osama bin Laden and his radical Islamic conspiracy.

That is one of the problems with the remarks by Gen. Boykin, first as commander of the Fort Bragg, N.C., training center and more recently as the deputy undersecretary of defense for intelligence. Addressing evangelical Christian audiences, he has denounced Muslims as worshiping an “idol” and not “a real god.” He said to a church audience in Oregon: “Why do they hate us? The answer to that is because we are a Christian nation.”

In another appearance, he named “Satan” as America’s real enemy, adding, “Satan wants to destroy this nation, he wants to destroy us as a nation, and he wants to destroy us as a Christian army.” He told an audience of Southern Baptists in Florida in January about capturing a Muslim militia leader in the 1993 U.S. intervention in Somalia, recalling an interview in which the militia leader had declared that Allah would protect him and his forces. Gen. Boykin said, “I knew that my God was bigger than his. I knew that my God was a real god and his was an idol.”

Some of his other statements have gone far beyond military matters. Discussing recent court decisions upholding the constitutional separation of church and state, he said, “Don’t you worry about what those courts say. Our God reigns supreme.” He ascribed George W. Bush’s presidency to divine intervention: “Why is this man in the White House? The majority of Americans did not vote for him. He’s in the White House because God put him there for a time such as this.”

Secretary Rumsfeld refused repeatedly to criticize him but later said Gen. Boykin has requested an internal investigation, and “I think that’s appropriate.” This was after Sen. John Warner, a Virginia Republican, and Sen. Carl Levin, a Michigan Democrat, chairman and minority leader, respectively, of the Senate Armed Services Committee, had asked Mr. Rumsfeld for an investigation. They said that inflammatory statements by a senior military officer “may easily be exploited by enemies of the United States and contribute to an erosion of support within the Arab world.” On a stopover in Bali, Indonesia, President Bush told a group of moderate Muslims that the general’s remarks “didn’t reflect my opinion” or “what the government thinks.”

Sen. Susan Collins, a member of the Armed Services Committee, supported the request for an investigation and said she agreed with Sen. Warner that Gen. Boykin should be reassigned during the investigation. She said in a statement: “There should be a clear definition as to when a department official should refrain from derogatory comments that do not reflect the views of the military and the administration.”

The question remains whether the Pentagon will conduct a full investigation or merely determine whether Gen. Boykin violated departmental regulations. If all he gets is a mild rebuke, it will be up to the Senate Armed Services Committee to make clear that the United States is not fighting Islam but is defending itself against a radical minority that should be just as offensive to the majority of Muslims as it is to the United States.