The letter landed like a thud on Saturday in the inbox of Harvard University’s president, Alan M. Garber. The message, from Linda McMahon, President Trump’s education secretary, conveyed an understanding of an emerging deal between Harvard and the White House that flew in the face of the terms the university had been insisting on. Dr. Garber felt he had made clear in recent negotiations that the university would not agree to pay the federal government to settle a monthslong battle with the Trump administration over antisemitism on campus and other matters. But Ms. McMahon’s Saturday message said the opposite. In...