Talk for yourself, this episode made me like Phlox very much. Not because of the Prime Directive issue but because he was portrayed as a real alien who neither has the human urge to help the Valakans nor the ability to see exploitation in the stable, symbiotic relationship between Menk and Valakans.
That's precisely why his argument is so convincing, he does not believe that the Menk are exploited or mistreated.
Back to your main point, the Valakans are not punished for anything. They are just not given an advantage over the Menk. You can't choose sides so you gotta stay out.
The Vulcans have been surely been asked again and again to help 21st century humankind deal with radiation sickness, to give them food, technology, etc. and I guess that their refusal to help humans (which might have made them appear like a nasty fatherfigure without any maternal elements) pissed us off. Enterprise started off with this very theme, distrust and tensions between the two species.
Yet it was right for the Vulcans to withold technology and resources that could have eased human suffering, just like it was right for Archer to withhold the cure. The only problem of Dear Doctor
was that is sounded social Darwinistic due to the Neanderthal comparison.
Of course you can argue that the Vulcans are baddies ... but this would make the whole Federation with its nasty Prime Directive a bunch of wicked psychopaths which is a line I naturally can't follow.