Thomas Magnum never actually left naval intelligence
Thomas Magnum has had psychic powers during the Vietnam war.
Due to the trauma, he had locked them away with his memories. They moderately resurfaced after the war. Ivan was already a dead man.
Ivan had four strikes against him. He engineered a major political assassination, which is bad. Worse, the attempt was discovered and failed. Even worse, Ivan was caught and identified as a Russian agent. Worst of all, there was no telling if he'd try again. The Russians had to believe Ivan was a dangerous loose cannon. By that reckoning, if Magnum hadn't shot him, Ivan was sure to end up at the wrong end of an umbrella tip. Higgins isn't really Robin Masters, but began writing "Robin Masters" books after Masters died.
Donald Bellisario, who should know, says in this interview
that Robin was never Higgins. He made it clear that Robin was a separate person. However, in this discussion on Magnum Mania, Jay Huguely is credited with the idea that when Orson Welles died in 1985, Robin also died, and that Higgins then worked with Robin's publisher to keep "Robin Masters" novels coming out. (V. C. Andrews and Robert E. Howard have both had continuing series based on "posthumous collaborations" from unfinished outlines or just freshly made up. In Masters' case, we can guess that Masters' novels took a decided upturn in quality after his death, with a skilled storyteller like Higgins at the helm.)