After Japan was defeated in the Pacific but before the use of the atomic bomb, was long-term containment ever considered as an alternative to amphibious invasion (and the large scale casualties that were anticipated?)

Nope. In January 1943, President Roosevelt issued a public demand for the unconditional surrender of Germany and Japan. No terms of surrender were offered to Japan until July 26, 1945, after Stalin, Truman, Chiang, and Churchill (replaced mid-conference by the new prime minister Attlee) met at Potsdam, Germany and issued the Potsdam Declaration - which was presented as a clarification, not a modification, of Roosevelt's original demand.