In "Dear Doctor," he wasn't really saying he thought the Valakians should die, just that he didn't think it would be responsible to tamper with the planet's evolutionary process when they had so little understanding of how it might unfold.
That would be fine. But that's not the message I got from Phlox. To me, he seemed pretty sure that the Menk were going to become the dominant species as long as the Valakians died out. That's hardly a neutral, objective stance. He didn't say, "I can't meddle because I might screw things up." He said, "I can't meddle because the Menk have more of a right to live than all the people who just asked me to cure them."
I really don't get it. The Menk, who weren't sick and dying, who didn't ask for anything, were more important to Phlox than the patients who were sick and dying and asked him for help.
They asked for a cure, he found one, and then he got all high and mighty on them and kept it away from them.
I really don't understand his decision. And it really didn't seem to me like the episode was meant to be ambiguous, Phlox seemed to be presented as absolutely in the right.
That's the feeling I remember getting from the episode.