The concept is bigger than us all... and neither did Archer, he just stayed out of the way the best he could...
I think you are right insofar that this is what the episode is trying to get at, but imo the writers did a clumsy job of it. To see the problem with Phlox's reasoning, I think it helps to change the scale a bit.
Imagine that a city, let's call it New Picard, has an influx of an immigrant population. They don't speak the language, and they are poor when they arrive, so they end up working a lot of menial jobs and basically become the city's underprivileged class. But they've improved their situation slowly over time, and seem to be on the brink of making a major step forward.
Then a devastating plague hits the city, and the immigrant population just happens to be mostly immune, while the currently dominant population will be decimated. You are living in a nearby city, let's call it New Sisko, and you have a cure. Can you justify not curing the New Picardians because, if you don't, the city's underprivileged class will likely end up as the city's dominant population, due in part to the decimation of the upper classes?
There are just too many false assumptions here, most of which can be applied to Phlox's situation as well.
1) The Valaxian's lives are worth just as much as those of the Menk.
2) The Menk may be having their "evolutionary awakening" because of their current interaction with the Valaxian's, not in spite of it. (Note: I'm not sure what is meant by the phrase "evolutionary awakening," and can't think of anything it corresponds to in the admittedly limited reading I have done about evolution.)
3) The Menk will certainly continue to evolve, in one way or another, even if the Valaxians are cured.
4) The Menk might end up being the dominant species even if Archer intervenes to prevent the immediate deaths of the Valaxians.
5) Speculation about how one species might or might not evolve in the absence of another can't justify allowing an entire species to die when those deaths are readily preventable.
That is basically where my thought process has taken me, though I'm quite sure that others in the thread know more about evolution and probably ethics than I