First, Phlox did not break any rule. He considered insubordination but didn't do it.
Second, The Breach reveals that your notion of Phlox being subject to human medical ethics is wrong.
Third, Archer could have chosen a human doctor but he chose an alien doctor for a good reason.
The emerging Federation is not a "homo sapiens only club". What we see in ENT is the slow coming together of species that differ and often cannot stand each other.