but it wasnt a dilemma of "should we help or not?" it was "we mustn't help because evolution-destiny tells us not to"
yes! exactly-the "dilemma" doesn't work, nor is it meant to even be a dilemma-from the presentation of the episode from Phlox' point of view, we are meant to see that Archer "saw the light" when Phlox approves of him for basically accepting his nonsense pseudoscience.
This wasn't like "Tuvix"-the viewer wasn't meant to wonder about the decision, they were meant to overlook or ignore the misunderstanding of evolution on display here and respect Archer's decision.