Gen. Abdel Fattah Sisi’sEgypt holds at least 40,000 political prisoners, secular democrats as well as Islamic extremists. His security forces have killed thousands — at least 817 at a single demonstration, according to Human Rights Watch. For three years, the Obama administration kept Sisi at arm’s length, working with his government on counterterrorism while expressing disapproval of its repression. No longer.