You can tell that the writers were very pleased with themselves in creating this fake, nonsense dilemma from the way the episode plays out.
Do you think the writers were too lazy to do some basic research on the subject matter (evolution), or were they actually aware that what they were writing was utter nonsense, but didn't give a shit?
I would guess from the way that the episode plays out, and the way evolution has been portrayed in the past in Trek(like in "threshold," which I think had one of the same writers as "DD?"), that there seems to be a basic lack of knowledge about evolution and how it works.
This episode's writers seemed to seriously think that evolution has some design in mind, and actually "decides" to favor certain species over others in bringing that design to pass.
I could be wrong. Just a hunch from the way the "science" is portrayed in this episode as compared to the way the usual b.s. technobabble pseudoscience is portrayed.
And like a few others, I really disagree that this episode's conclusion is meant to be "ambiguous." Phlox is supposed to be seen as in the right, and Archer is supposed to have shown that he "matured" by making the more intellectually sound, less emotional decision.
Why do I think this? Look at Phlox's log entry where he says that he may have "underestimated" Archer and how impressed he was by him. He's speaking for the writers there.
And as usual in "dear doctor" threads, I want to recommend SFDebris' review of this episode.