About "Dear Doctor":
The species change by adapting to their environment.
Phlox discovered that the Menk were adapting toward incresing intelligence under Valakian influence.
The Valakians' disappearance would change the Menk's environment and Phlox couldn't have more than some vague predictions about the Menk evolution in the new circumstances - unless he could see into the future. And then, there are imprevisible variables - an asteroid hitting the planet, a disease - that couldn't be surmounted by the primitive Menk.
By refusing to give the Valakians the cure, Phlox+Archer prejudiced both the Valakians and the Menk:
The Valakians were denied a chance of survival;
The Menk survival/evolutionary future towards higher intelligence has become more uncertain - with the Valakians they were sure to become smarter across generations; without them, they MAY evolve in that way.
The episode is trying to create a moral dilemma by saying that under the Valakians, the Menk wouldn't evolve at all - this is directly contradicted by the episode itself (which showed the Menk developing at an impressive pace).
Even if we consider this assumption (and the bad science on which it is based) as true, Phlox+Archer's decision is still morally wrong (disgusting, actually) - they condemned a species to death so that another one has a chance of flourishing.
This is analog to letting a person die (a person that could be saved with certainty) so that a dr Mengele waana-be can chop her up for spare organs and use these organs in order to try and save another person (an action which may or may not succeed)./QUOTE]
Phlox never said the Menk's increasing intelligence was a result of the Valakians' control over them. In fact, he implied that the Menk's advance was being impeded by the Valakians.
Phlox: I've been studying their genome as well, and I've seen evidence of increasing intelligence. Motor skills, linguistic abilities. Unlike the Valakians they appear to be in the process of an evolutionary awakening. It may take millennia, but the Menk have the potential to become the dominant species on this planet.
Archer: And that won't happen as long as the Valakians are around.
Phlox: If the Menk are to flourish, they need an opportunity to survive on their own.