To my mind killing an Admiral in a combat zone doesn't really qualify as an assassination. The Japanese did engage the
339th, they just didn't do it very well. Sending orders I guess could qualify as assassination, but frankly he was a enemy
member of a hostile military in a state of war with the US.
Considering how the public still felt about Pearl Harbor, I imagine the decision to take him out didn't cost FDR much sleep.
Incidentally killing an admiral or general, or as a target of opportunity like Lord Nelson was, would not be an assassination. Specifically intercepting and killing him as the sole purpose of the mission would be.
Put it this way, if that had just been a G4M with A6M escort there is no way we'd have bothered to try to intercept and shoot it down. It simply wouldn't have been worth the risk and effort to pull off successfully without Yamamoto being on the plane.
In no way does this make it nefarious, dishonorable or any such thing. It is just a clinical description as an attack planned and targeted at killing an individual.