We already creating headcanons about morality values of something that we only saw hints until now? But, about the WG, it is show plenty of times that Admirals and Vice Admirals have the power and the capability to decide to kill soldiers that fail to fullfil their duties, as well as civilians and pirates if they think it's in the escope of their duties. Kuzan was willing to kill Saulo (until it was show that he was alive), Akainu killed the deserters and was about to kill Coby as well in front of everyone for insubordination, as basic examples.
Those actions are much more medieval and actually very similar to how generals and leaders acted in ancient japan, china and korea. Akainu is considered more extreme but he has the power to take those decisions and it's accepted by his subordinates. You can even look at how everyone reacted when Akainu killed the civilians: no one acted as if he did something illegal or beyond his powers but most acted as if he was taking things too literally. The same happened when Coby tried to stop the war: Akainu took the decision to end his life in front of all the marines and no one acted as if he didn't had the right (but again everyone in universe acted and recognize that he can and will do everything for his justice).
Do you see Akainu trying to hide or worried about killing a navy soldier? Of course not, because he has that right. And frankly, it's even a light punishment. Try to research the origin of the word decimate.