You know, it occurs to me. A future series can revisit that world and we can see if the Valakians died out or if the Menk flourushed. There are multiple possibilities...
1. Archer and Phlox was right, and the Menk flourished.
2. They were partly right... Valakians died off, but so did the Menk. Either because they couldn't adapt or the Valakians decided if they were going to die, they'd take the Menk down with them.
3. The Valakians found a cure on their own. That could lead them to either keep the Menk subservient, or the Menk rise up and kill the Valakians.
4. They found a cure, but because the Menk helped them out throughout the entire crisis, they get more and more liberties to the point where they are equal in everything.
Personally, I'd like to see option 4 because not only does it send strong message that everyone CAN get along and be equal, but it would clear Archer and Phlox from all the people who called them perpetrators of genocide.