I understand Stevens' qualms about targeting Yamamoto directly- it smacks of assassination which in some fashion or other we're supposed to be against and eschew.
But I think that some of the history of the Japanese army when outside of Japan precluded regarding them as worthy of such "rules of war" or foreign policy constraints on our part.
First, Japan wasn't a signatory to the Geneva Convention until after 1945, which was a tacit admission of intent to violate its provisions (rules internal to the Japanese Imperial army notwithstanding, and not followed off the home islands anyway).
The behavior of the Japanese army, beginning in 1910- the wholesale rape and murder of civilians in Asian countries they attacked, invaded and occupied, such as the rape of Nanking in 1937, the Bataan Death March, Panjiayu tragedy, the war crimes in Manchukuo that began in 1931 (where all the bestial acts of the Nazis in their concentration camps were committed by the Japanese occupiers) and elsewhere in Japanese-occupied parts of China, and a long list of crimes against civilians wherein mass murder and rampant rape of women and children were committed by the Imperial Japanese army, and the attack on Pearl Harbor by creeping up in the dark with a military force with no prior declaration of hostilities, pretty much led Americans and our military leadership to conclude that they weren't worthy of a break. It was thought that blowing up Yamamoto had tactical benefits in the Japanese army's morale, but as it turned out they were clearly going to fight to the death in any case, along with their civilian counterparts, which engendered the nuclear attacks on Hiroshima and Nagasaki.
Why were they so inhumane and behaved in such despicable, unjustified and bestial ways? Some who have studied it believe the military assumed for itself the prerogatives (but not the honor or discipline) of the ancient Samuri; others believe it was that the Japanese society was so completely non-individualistic that no one had or needed a personal code of ethics or individual sense of morality, the culture dictated these in detail to every citizen, who were obedient to those dictates and is what kept order and structure in the society. Once apart from that environment (that is, off the home islands), the absence of any personal ethics left the army uncontrolled because the individual soldiers had no personal sense of honorable behavior and outside their country there was no externally applied code, the internal rules of the army notwithstanding. So killing Yamamoto to some took on the nature of killing the lead dog in a rabid pack, and the P-38's were dispatched to do so.