First I will say that I did not read everything posted about this topic.
I am currently in an ENT rewatch and just saw this episode the other day. I have also had this discussion a few times. Here goes:
Though I don't know if I could have done what Archer did, I think what he did do was right. He was smart enough to have a "prime directive" before there was such a thing. Maybe listening to what T'Pol had said in the past about interfering sunk in.
I see both sides of the story but I would have sided with Phlox and Archer on this one.