Dear Doctor is not about biology, it is about the power relations between the two species. Human ethics imply that we gotta treat the Valakian disease but also imply that we free the Menk. This is obviously not possible unless you wanna rule the planet and giving one group an advantage over the other is not possible either. So the Prime Directive, not existent yet but embodied in the ways Vulcans and Denobulans handle these issues, would forbid interference. That it is not humans but the species which have more deep space experience who came up with interspecies ethics was another great idea of ENT as Trek is often too anthropocentric.
About the ending, I would have preferred the original draft in which Archer is not convinced by Phlox and treat the Valakians. He adapts interspecies ethics a bit to quickly, he should mess up a few times before he sees its merits.
Dear Doctor is for me probably the best ENT episode, not at least because it is the most counterintuitive Prime Directive episode. You can't follow your hunch like Archer (sympathizes with the Valakians) and Cutler (sympathizes with the Menk) do, you gotta use your brain like Phlox does.