I think Phlox was speculating that as the Menk evolved towards full sentience, they would become dissatisfied with their role, and this would potentially lead to real oppression of them by the Valakians, or genocide against them by the Valakians, or long term war between the two.
But it was only speculation.
The future is forever inscrutable. Who knows what path it may take, what turns and twists and unforseen factors lie ahead? Based on some dodgy speculation, Phlox decided that he
knew what was best for two entire species. And he took it upon himself to be judge, jury and executioner for the Valakians. And then he and Archer have the temerity to congratulate themselves for "Not playing God"? I'd hate to see their idea of actually playing god.