I think a lot of the supposed inconsistencies in Martin’s morals regarding Jon during season 5 can be boiled down to the writers not knowing how to write characters that aren’t disgusted by or dehumanize Jon for things they told him to do, things they were okay with him doing, things they themselves have done, and things they were okay with others doing. Which they then shoehorn reasons for them to be right about why their hypocrisy towards him was correct, even though they were contradictory to prior actions he had taken.

But also I think characters in the Magnus Archives aren’t supposed to be seen as morally correct unless they’re actively disgusted by or dehumanize Jon and Martin is supposed to be the ‘human’ one of them so of course he had to be.