Yeah, they pulled the prime directive out of thin air, and made it seem like the main motive of the prime directive was actually the stupidest fringe case, instead of what it really was, a moral imperative not to manipulate politics of other countries for your own interest.
I'm with you on this one. I thought the PD speech felt a bit forced into the script, especially when Archer says "some kind of...directive."
The fact that they chose not to share the cure didn't really bother me story-wise. In fact, I found it rather interesting (though I didn't agree with the decision). But I can certainly understand why some would be bothered by it.
Now it would have been far more interesting to me if Phlox stayed completely silent about the fact that he found a cure, and then the episode could have ended on a deliberately dark note. He almost didn't tell Archer about it anyway. It would have been better to me if the writers took that one step further. Ah we'll.
I thought the episode was okay overall. I didn't love it, but I don't hate it so much that I'll stop watching altogether. I have enjoyed reading all of your thoughts!