One rationale for avoiding assassination or targeting of enemy leadership for military strikes is that it can leave the "other side" with no one who is able to "turn the machine off" in the advent of surrender. This makes perfect sense in a conventional war of limited aims; in a total war or against non-state actors it may or may not be an appropriate. It depends on whom you are dealing with and the larger strategic picture.

In WWII Japan had approximately 2 million men in its armies in China and Southeast Asia with a ferocious track record, even in engagements where the Imperial Army had taken a severe beating ( against the Soviets at Khalkin-Gol/Nomonhan and Chiang's all-out defense of Wuhan). It was feared by Allied leaders that these sizable forces would simply go down fighting even if the home islands fell. Therefore, Stimson and Marshall wisely kept the Emperor's palace off the target list for conventional bombing, starting with the Doolittle Raid, and Tokyo off the target list for the atomic bomb.

In Europe, Allied intelligence was aware of the plot to assassinate Hitler by Stauffenberg's conspirators, thanks to Allen Dulles contacts with Gisevius and the Abwehr in Switzerland, but nothing was done to encourage the plotters beyond accepting their information. In contrast, British intelligence took out the dreaded SS intelligence chief, Reinhard Heydrich, via assassination not because of his crimes or intel role but because of his very effective ( in a political sense) occupational governorship in Bohemia and Moravia.

In postwar eras, the U.S. and/or the CIA has been accused of complicity in the assassinations or deaths of Nkrumah, Ngo Dinh Diem and Salvador Allende. In each case, there were local actors with their own agendas involved in the overthrow who were beyond U.S. operational control ( and whose necks were in the noose if the coup failed). Where American control of such covert operations was direct, as against Arbenz in Guatemala and Mossadegh in Iran, no assassination actually took place. Operation Mongoose, about which much has been written, was a spectacular failure as Castro's continued existence in elderly dotage attests