Reacting to the article and not OP here, also spoilers:
I'm sorry, I know the movie was long, but did OP miss the Bronze-age Darth Vader with bones on his head? The very classic Nolan ending twist that Athena was a PTSD hallucination of the Trojan woman they killed? The constant and obvious murdering and pillaging that Odysseus and his crew do? That the Trojans were wearing white and the Greeks were wearing black? The very obvious scene where all the people that they have killed tell Odysseus that he is a bad guy and then they all go running after him and the crew?
Like, to me, I felt that it was over-the-top obvious, almost embarrassingly so from such a director, that the Greeks were the bad guys. He could not have communicated that more or better to my eyes. He comes out and says so at the ~90% mark. It is very clear.
But, and I apologize if I am also guilty of this sin with the article, it seems that he does not even still do enough to communicate that to many viewers.