I think you can call Yamamoto's attack an assassination if you want and nobody would bat much of an eye. Either way it is legal by even modern standards — Yamamoto was killed in the field of battle, he was a military officer, he was killed by marked military forces during a time of declared war. That his death was deliberate and planned doesn't seem to matter much. This is considered by international law a markedly different situation than killing civilian politicians, or killing even military combatants by covert forces. This thesis goes into some detail on the distinctions made; it notes that Yamamoto's killing was probably legal by even modern standards (and certainly by standards of the time) whereas the killing of Heydrich by un-uniformed soldiers is much more problematic and probably illegal under international law.

I haven't read that interpretation of the operation. The concerns I am familiar with regarded a desire to not give away that the US had broken the Japanese encryption that made the interception possible, and that subsequent flights were made to make it look like the interception of Yamamoto's transport was a lucky break and not a deliberate operation. Yamamoto was a uniformed enemy combatant in a marked military plane, so I believe that the legalities of war were followed--but I am not an expert on the specifics of that particular question.

Do you have a source for this interpretation? I don't mean to challenge you in the least, but knowing where a line of thought comes from can shed some light on what kind of question is being raised.