I dunno...I guess I'm left feeling that whether or not it's okay to violate the Prime Directive is rather akin to the issues brought up in the Futurama episode "Godfellas".
Still love this line...it applies to playing God, but might just as well apply to violating the Prime Directive - "When you do things right, people won't be sure you did anything at all."
"Dear Doctor" is simply a terrible episode.
Phlox has made the determination that the Menk can't evolve with the Valakians around even though we see that the Menk have language, the ability to use logic and work in hospitals and even use touch screen computers.
Phlox came off looking like he had no idea what he was talking about and Archer blindly followed him.